Yes. The trans will certainly need a 300M input shaft to sustain the instant torque from the blower. The Bonne has a couple hundred more pounds to lug around behind it.
I personally never understood the people ratting on top swaps. L36s have been known to sustain the abuse just as well as an L67. The key lies in the tuning. It's a delicate process. But the car will produce more power and retain really good driveability out of boost as well. Providing you don't cam it right off the bat, many mention that you might see a small increase in fuel economy as well if you keep your foot out of it...
But as we all know, that ain't easy!!
Also, Matt really knows his stuff. I'd take his advice over mine.

However, you can try running corn juice until you can afford an intercooler. But you should really consider one. To give you an idea as to how effective they are at killing knock, if you just buy an intercooler up front, you can drop right to a 3.2 pulley. The GTX GP concept used intercooling, but they stripped it off and put on the dinner plate pulley because it was outrunning Vettes.