Ken...I experienced the same problem,only I hadn't planned ahead!
I fitted my booster/mc
before I fabbed my
crossmember . As you can see I had to put a 'little' offset on the left side.

I realise my trans is a TH350C but the problem seems to be similar.
I guess you may have to consider doing the same.
I have also had some other problems with my disc brake kit,similar to the ones you described earlier.
I don't think this is common to just the CPP kit.
Mine was from Speedway....