You will find that the 3500 mounts will be different than the 31/34 hundred mounts. You will need to fabricate some stuff to make do. The TB situation will be not resolved with just a TB swap, cables will be an issue. You will need other GM parts to complete that task. The coolant sensors will need to be addressed. The lx9 uses a crush sealing washer with a different smaller thread design. The lower intake doesn't have provisions for the other sensor. The power steering pump will not work with the setup you have going in. Will again, need to source another GM vehicle for that.
The rear tgp manifold bolts may not work well due to it being to long, I suggest just picking up studs and nuts with locking washers.
I highly suggest going with different larger ex.manny's, those stock ones even extremely ported will be restrictive and then be prone to cracking due to the extreme porting.
I have a 3400 Van UIM AND a 3400 Grandam LIM here... I am willing to part with it if you are interested. Shoot me an offer, I am located in MI.
Are you SURE that the power steering pump wont work. Everybody says that it won't bolt up. But it looks to me like it will. Is there another that will?
I won't be using tgp manifolds... too small. I'm going to use 3400 manifolds and block the DP, weld a T4 flange on the crossover and fab up a downpipe. At least, that's the plan for now... If I don't like it I'll just build an exhuast.
I've already bought a LP3100 UIM and fuel rail from a 2000 malibu, a 56mm TB from a Montana, a TB cable bracket from a 94 grand prix complete with kickdown cable mount

and ICM mount bracket. wot-tech sells a CTS adapter.
I'm going back tomorrow for 3400 exhaust, 94 gp heater lines, passenger side dogbone mount, motor mount, and a/c compressor.
As for the motor mount, that's something I hadn't counted on and I'm working on it. I'm going

I cant think of anything else right now...