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Seriously thinking about doing the 3500 manifold swap to my 94 3100, as I'd like the extra gained low end vs just a 3400 manifold swap. Below I'm listing various items that need to be addressed. If I missed any please post and I will add them. I don't know the answers for sure on some of them, so I will update the sections as I go. Hopefully this will turn into good reference others can turn to later. This is pertaining to a gen3 small port swapping to large port lower (3400) manifold with a 3500 upper. But most of this will apply to other 3500 swaps. Ok so here we go....
Items in Italics need additional info, help please!!
Vacuum Sources: You'll need a 1/4" NPT tap to tap the vacuum port by the EGR mount. It had some evap soleniod or something there. Put a 1/4"MPT-1/4" barb fitting in there with teflon tape on the threads. Then T or Y it off to the FPR, and the metal pipe that goes to the transmision modulator. Use 1/4" hose to the trans modulator, and to the FPR, 1/8" should be fine since it's a small tube anyways. You could opptionally JB weld in a metal tube instead of tap, and put hoses on that if you wanted to do that... Or if the vacuum nippe by where the brake booster nipple is came tapped and fitted on your 3500 plenum, you can use this for one of the vacuum sources. Mine came tapped, but I'm using it for my cruise control.
EGR: Is a side mount. Adapter from http://www.feavs.com/ or the "$5" adapter which uses the EGR "plate" from a 3.1mpfi motor that goes between the EGR and intake manifold.
TB: Adapter needed & a TB. The 660 store has an adapter to use their 65mm TB or a stock one.
Coil Pack Mount: Mounts in same place, but without 2 bolts on the top.
MAP Sensor: Re-use old; you'll have to add a tube or tap the hole in the manifold and connect it to your old MAP. You could also use the new MAP if your plenum came with one, but you'll need the proper connector which can be found on 98+ caviliers.
Bolts: You can re-use your lower bolts for the new large port LIM. For the 3500 plenum, NAPA has a bolt rack, take one of your old plenum bolts to the rack to match up the threads, and then get ones that are 2.565" (65mm) long, M8 1.25 thread pitch.
FPR Clearance: Grind the neck of the plenum down so FPR has room.
Port Match: It's a good idea to port match the manifolds so there is no restriction in flow between them.
Gaskets: What the lower part is, use the gasket for that. Example, if you have 94 3100 heads, use a LIM gasket for those heads, not the gasket for the 3400 heads/LIM. If you are putting 3400 heads on a 3100 block, use 3100 head gasket. And of course the UIM gasket you'd use a large port 3400 upper gasket. If you are using the 60v6 store TB adapter, then if you use a stock TB, you need to remove the o-ring for the side that mounts the TB, and get a gasket for the year/kind of TB you have. If going with the CNC 65mm, no gasket is nessasary.
Large port lower manifold required, possible issues:
Updated gen3 Heads: If you want to get rid of your original 3100 heads, and go for the 3400 better flowing heads (have roller rockers {not roller tip though} larger intake valves and other stuff), then you'll need to get a newer 3 wire ECT/CTS. The newer heads do not have a place for the sending unit that shows the temp on your dash. Putting a 3 wire one in the thermostat housing allows both to work from one sender. You'll need to re-wire your 2 connectors to plug into it. Check out 3400swap.com guide for more specific info. If you are doing the head swap, then you do not have to worry about rocker clearance below:
Lower Manifold Rocker Clearance: If you have the gen3 early stamped rockers (that are not roller fulcrum), getting a 2000+ lower will help with clearance issues. You will likely have to grind more to make room for the rockers, but the 2000+ is already ground some to get you started. Putting a breaker bar on the crankshaft pulley and slowly turning the engine by hand and watching the rockers or using a feeler gauge is essiential to make sure you don't hit and collapse a lifter and put aluminum shavings in your motor when done!
Lower Manifold Coolant pipe: You'll have to get a new coolant pipe for the lower manifold, this is the pipe that has the screw on metal peice that the black metal pipe clips into. The one that you always have to get a new screw in peice when you take it off. This way if you take it off again you just pull the pipe out of the manifold. If you want to keep the threaded dohookey setup, then make sure your lower manifold is from a 1996-1998 3400 van motor, as it will be the old style. Or tap the new manifold... I figure cost of the new snap in style metal pipe that doesn't use the screw peice is about the same, and will likely not need to be replaced every time you take it off like the screw on peice does (the insides crack apart).
Stock PCM: With this setup, the ECM should be able to cope. A 56mm TB should be fine, larger might work ok, 65mm is max you could get away with unless you have access to tune the ECM. Since 94/95 cars don't have access to tuners, this has to be considered.
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Hopefully this covers/will cover it all. Please help with the stuff in Italics. I want a boost on my old motor, and would like to go the 3500 upper route over the 3400 to get some extra low end to help out with the terrible gearing in my granny tranny, and from what I hear, it helps even more on high end than the 3400 too.
Items in Italics need additional info, help please!!
Vacuum Sources: You'll need a 1/4" NPT tap to tap the vacuum port by the EGR mount. It had some evap soleniod or something there. Put a 1/4"MPT-1/4" barb fitting in there with teflon tape on the threads. Then T or Y it off to the FPR, and the metal pipe that goes to the transmision modulator. Use 1/4" hose to the trans modulator, and to the FPR, 1/8" should be fine since it's a small tube anyways. You could opptionally JB weld in a metal tube instead of tap, and put hoses on that if you wanted to do that... Or if the vacuum nippe by where the brake booster nipple is came tapped and fitted on your 3500 plenum, you can use this for one of the vacuum sources. Mine came tapped, but I'm using it for my cruise control.
EGR: Is a side mount. Adapter from http://www.feavs.com/ or the "$5" adapter which uses the EGR "plate" from a 3.1mpfi motor that goes between the EGR and intake manifold.
TB: Adapter needed & a TB. The 660 store has an adapter to use their 65mm TB or a stock one.
Coil Pack Mount: Mounts in same place, but without 2 bolts on the top.
MAP Sensor: Re-use old; you'll have to add a tube or tap the hole in the manifold and connect it to your old MAP. You could also use the new MAP if your plenum came with one, but you'll need the proper connector which can be found on 98+ caviliers.
Bolts: You can re-use your lower bolts for the new large port LIM. For the 3500 plenum, NAPA has a bolt rack, take one of your old plenum bolts to the rack to match up the threads, and then get ones that are 2.565" (65mm) long, M8 1.25 thread pitch.
FPR Clearance: Grind the neck of the plenum down so FPR has room.
Port Match: It's a good idea to port match the manifolds so there is no restriction in flow between them.
Gaskets: What the lower part is, use the gasket for that. Example, if you have 94 3100 heads, use a LIM gasket for those heads, not the gasket for the 3400 heads/LIM. If you are putting 3400 heads on a 3100 block, use 3100 head gasket. And of course the UIM gasket you'd use a large port 3400 upper gasket. If you are using the 60v6 store TB adapter, then if you use a stock TB, you need to remove the o-ring for the side that mounts the TB, and get a gasket for the year/kind of TB you have. If going with the CNC 65mm, no gasket is nessasary.
Large port lower manifold required, possible issues:
Updated gen3 Heads: If you want to get rid of your original 3100 heads, and go for the 3400 better flowing heads (have roller rockers {not roller tip though} larger intake valves and other stuff), then you'll need to get a newer 3 wire ECT/CTS. The newer heads do not have a place for the sending unit that shows the temp on your dash. Putting a 3 wire one in the thermostat housing allows both to work from one sender. You'll need to re-wire your 2 connectors to plug into it. Check out 3400swap.com guide for more specific info. If you are doing the head swap, then you do not have to worry about rocker clearance below:
Lower Manifold Rocker Clearance: If you have the gen3 early stamped rockers (that are not roller fulcrum), getting a 2000+ lower will help with clearance issues. You will likely have to grind more to make room for the rockers, but the 2000+ is already ground some to get you started. Putting a breaker bar on the crankshaft pulley and slowly turning the engine by hand and watching the rockers or using a feeler gauge is essiential to make sure you don't hit and collapse a lifter and put aluminum shavings in your motor when done!
Lower Manifold Coolant pipe: You'll have to get a new coolant pipe for the lower manifold, this is the pipe that has the screw on metal peice that the black metal pipe clips into. The one that you always have to get a new screw in peice when you take it off. This way if you take it off again you just pull the pipe out of the manifold. If you want to keep the threaded dohookey setup, then make sure your lower manifold is from a 1996-1998 3400 van motor, as it will be the old style. Or tap the new manifold... I figure cost of the new snap in style metal pipe that doesn't use the screw peice is about the same, and will likely not need to be replaced every time you take it off like the screw on peice does (the insides crack apart).
Stock PCM: With this setup, the ECM should be able to cope. A 56mm TB should be fine, larger might work ok, 65mm is max you could get away with unless you have access to tune the ECM. Since 94/95 cars don't have access to tuners, this has to be considered.
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Hopefully this covers/will cover it all. Please help with the stuff in Italics. I want a boost on my old motor, and would like to go the 3500 upper route over the 3400 to get some extra low end to help out with the terrible gearing in my granny tranny, and from what I hear, it helps even more on high end than the 3400 too.
Neato. Yup grind the TB neck down so the FPR clears, already got that up there. Port match is a good idea, I'll throw it up on the list, I planned to do that anyways (gasket match both upper & lower where they meet each other). Map, re-use easy enough, but I thought people who ordered theirs from GMPD it came with one installed, maybe it was just ones from car-parts.com? I'll update the list. What is the IAC hole on the 3500? is it the #5 here on 
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