[dsraven]

ok, just so we are on the same page here
-59 chevy fleetside
-stock underpinnings
-454 big block with 200r auto trans
-the original trans cross member is still in there but the trans pan is almost sitting on the pan
-you have a tubular cross member installed at the rear of the trans but it doesn't provide enough support for the frame at the cab mounts/spring perch areas
-you have side mounts on the engine (guessing)
-your engine is so lumpy it hardly idles
-you want to swap out your torque converter for one with a different stall (guessing)
-trans isn't gonna come out without getting rid of the old cross member
-there is no room above trans or between engine and firewall etc to jack the engine up enough to get the trans out over top of the old cross member (guessing), or the trans shop is not happy about having to mess around with it so they would over charge you (guessing)
-trans shop says hack the member out of there no biggie (guessing)

-what would be the plan once the trans is fixed? daily driver, weekends, burnouts fairly often, lots of high torque stuff?
-have you thought about a different cam to make drivability better rather than swapping the converter?
-do you like the lumpy engine so you would rather keep it that way and change the trans instead?
-when you say get the truck back to your mechanic buddy for repair, how far away is that? you don't wanna do that because of the long distance to drive or because of the engine drivability issue or you just can't get the time scheduled to get that done?
-are you sure the engine is awesome and no other problems with it or you are sorta hoping for the best in that dept? do you know any of the other internal components? wouldn't want to see you change the trans for drivability then find out the engine is a full race thing and not really great for what your driving style is, or maybe your driving style is full race, dunno.

my 2 cents would be
just get the truck to your buddy and fix it the way you want it and it will be strong. if you have a big torque engine you gotta make sure your frame etc will handle it or it will become one of those "if only i woulda" things that can suck time and money. you may also wanna ensure your brakes etc will handle the duties assigned by the big block engine. if you gotta cut the member at the trans shop tell them to use a zip disc for a clean straight cut and leave the removed piece for you so you can possibly graft it into something you can modify and re-use when the truck gets home. a short drive with the member removed won't kill the truck most likely. not a long term thing to do though.
post up some pics of the actual problem and maybe we can find some answers