if your really keen on actually doing this id think it through a bit. stroking involves a full rebuild - as you mentioned - with the crank, rods and pistons being replaced in order to increase displacement to 4.2L (c.o.m.e. stroker) or 4.3L (bradley stroker).
other parts such as the cam+timing gear, heads and rockers+valve springs usually get changed also to make the most of the combo.
if you get a decent size cam, when you stroke the V6 i would forget about getting twin t/b's, i know from personal experience they dont work well. they are more designed to be used on un-opened engines.
the box will be fine, depending on its current condition and the use (or abuse) it is used for once the stroker engine is in place. i had a completely stock 'box behind my stroker for a good 6 months without any dramas at all and even up till the day i took it out it was still fine (this is a 'box with 200k on it too).
for peace of mind though, and a bit more fun, i replaced the 'box with a much stronger rebuild one with all the goods (shift kit, valve body, corvette servo's, steel pistons, performance sprag and beast, performance friction kit,etc...).
as for anyone that does the rebuild, just get c.o.m.e. to build it. as you'll find out if your serious about it and get some quotes it costs quite alot to get the engine built at an engine builder/mechanics and c.o.m.e.'s prices are pretty reasonable in comparison.
there's not really anything more you "need" to change, other than getting a suitable tune to run the stroker engine, everything else will be done in the rebuild.
