I've got nothing but a stock CSI I can draw parts from. My goal is the best 3.5L bang for the buck. I do like the idea of incorporating the D-Jet logs though, and it would save the cost of the booster. Also- From previous posts, megasquirt sounds appealing.
So you don't have the 735 engine you mentioned in your earlier post?
The best "bang for the buck" 3.5 job depends on how much "buck" and time you have.
The best-performing 3.5 is a M90 block with a B35 head, (ideally with custom pistons) a log manifold with 320i intake runners, running MegaSquirt or Motronic 1.3 with a WAR chip. That setup will provide ~200 rwhp, rev nicely, and run quite well in a variety of circumstances. However, as you noticed, it is a very specific set of parts from several cars and several eras. It takes time to get the whole thing together, and about 3k all in. You need some sort of tuning capability, so a MegaSquirt or modified Motronic system are required, unless you are going carbs.
The second-best running and the easiest 3.5 swap is a straight M30B35 and Motronic 1.3 swap, including the manifold. As previously mentioned, it does require the 2002tii booster, but everything else bolts right up. There is no customization required and virtually no special wiring. You can pick up a complete M30B35 with uncut harness and DME for under 1k easy, then the booster (last I looked) was ~250$ used. I went this route. If you have done it before, you can do it in a weekend since there is no custom fabrication. If you go this route, rather than MegaSquirt, I'd go for a WAR chip, which allows you to program the Motronic yourself exactly like MegaSquirt. You even get to switch to a MAF as part of the deal, which allows you to junk the horrible AFM.