Originally Posted by Retro Grouch

I just test fit any JIS square taper bottom bracket that I happen to have on hand. Then I estimate how much longer or shorter spindle length I think that I need.

The caps usually come with the crank but they're a generic size and thread so you can use caps from any old crank. They're only cosmetic anyway so you don't really need them. Newer allen bolt-style bottom brackets are usually designed to eliminate the need for the caps.