On the trucks I've been involved with a V8 swap in to, there really wasn't any signifigant difference in the ride hight after the swap. As far as boxing goes, unneccessary on a street truck with stock suspension. I helped a guy put a pretty wild 355 smallblock in a '49, we had more problems with getting it to hook up than any frame twist issues. Now, if you were racing it or maybe installing an IFS, I could see boxing it. Getting the engine placement and steering box clearance are the #1 issues with doing this swap. On the last one I was involved in, we used a set of Rams Horns cast iron manifolds, and still had to move the steering box to get them to clear. I have heard that the steering box for a '57-'59 will bolt up in the stock location, and clear the engine, but can't confirm that.
As far as using a manual, I see no problem with it. We ran an SM420 behind that 355, it worked just fine.
