ok. you have several questions here so lets break it up. start with the engine. there are a few sprint cars here that have seen great results out of the engine you have in your car. as much as 450 hp and you save 200 pounds on the car by keeping it the way it is. if you want to go bigger its just your choice. both engines will fit with minor modifications to frame mounts. you'll need a set of 400 frame mounts and keep the 6 cyl. mounts for later use! that said lets move on to the next question. you can convert from a 3 spd to 4 spd no problem. some have used the 3 spd crossmember on the 4 spd but i have yet to do so. upon visual inspection there is isn't much difference! the only one i can see is the hole location in the crossmember being roughly 1/4" different. next question of using a 4 spd with that spline combo. the only thing you would need to change is the input yoke on your driveshaft. you should use the one that comes with the trans. just install it onto your drive shaft with new u-joints.
now for your bellhousing. it will work no problem! i have my 3 spd bellhousing bolted to my 4 spd at this very moment! bolted right up no problem! might want to spray a bit of wd40 in the holes before you thread the bolt in!

hope this helps you. if you need more help, others here have converted to 428"s and can give you more specific info on the exhaust issues and such but you should have no problem with whatever you choose!