I had to address the same plumbing issues with my Vortech conversion. I was able to use the blower to TB tube but had to fabricate my air inlet in a very similiar way that you did. How hard was it to make the brace for the engine bay. I have been thinking of something like that from Jay at Mustang Depot.
I got the brace from Laurel Mountain Mustang http://cgi.ebay.com/ebaymotors/65-66-67-68-69-70-MUSTANG-SHOCK-TOWER-BRACE-NEW_W0QQitemZ120366636673QQihZ002QQcategoryZ34200QQssPageNameZWDVWQQrdZ1QQcmdZViewItem
When I got it I soon found out that it fit like crap. I decided to cut it at every weld and weld it back together while attached to my car. I bent the main bar up a little for distributor clearance and I bent the drivers side tower to cowl bar up a little to clear the intake manifold. I tacked it all together on the car and then took it off for complete welding. It fits like a glove now and I can pull the distributor with it installed.
dcstang67 would you mind posting another picture of the passenger side monte carlo bar above the blower tube? How much clearance do you have? Did that take any mods on that side to fit?
Keep in mind that I made the brace fit first and then made the blower tube to fit after. I also clocked the compressor housing on the supercharger to fit. There is about 1/2" of clearence above the pipe.