I noticed today that the reinforced frame section right behind the trans has had about 1/2 inch of washers placed on the bolts. Looks as though it has been shimmed up to allow for the exaust to run in between the body and this support. Anybody know if this defeats the purpose of this additional support or is this OK to do?

it should be fine. Hotchkiss makes one that is dropped if you don't like the washers.
http://home.comcast.net/~Jimragtop2/pipes/exhaust2.jpg

do you still need it if you have sub frame connecters