Yes, Drew had to deal with all those problems.
I got a 2002 TII booster which is smaller in diameter to run with my Webers but still had to get shorty stacks because they would hit the booster. Also presents a tuning issue although I'm not real sure how big a deal that is. Pierce Manifolds in CA is the best supplier for all things Weber and great people if you need help. They also have a couple CD's on tuning. Best I've ever found.
https://www.piercemanifolds.com/
I have since changed to a Hydraboost system by GM. Not the BMW version. I was in fact getting the hoses made today to make that work. This was supposed to solve my interference problem with the Webers but the reservoir on the master was still too tall to clear the Weber air horn. So now I had to get a different master that has a remote reservoir that I can mount on the fender or firewall. Geez, it's only money......
Just got the hoses today in fact to do a little better job of hooking up the heater. Like Steve says many do not and just by-pass it. If you don't you will always get a small amount of heat on you feet. With that said you can do a heater control valve in many variations. I have a manual one in Atlanta. There is a write up on this forum by Rob Seigel on installing and electric solenoid valve. He lives in MA. MAybe thats why he wanted an electric one. To cold to open the hood to move the lever on the manual one. It gets cold here but more importantly I DRIVE my car. Went to Colorado in 2014.
What you have to do is find hoses that have the right inside diameter and then find hoses with 90 degree bends. You will then have to cut and fit to make them go where you want.
I use the long hose from the 6 series cars and then made an adapter out of copper plumbing pipe to make the bend to the hose for the back of the cylinder head. See photos. Part numbers and show you what they look like. Notice the 90 bends. Use those to go down from heater core connections.
HTH,
Gary