B18c1 in a 88-91 Civic Question

I am planning a motor swap for my 91 Civic hatchback this December. I was planning to buy a b16a1 complete swap and a b18c block separately, then switch the b16 out in favor of the b18. Will I run into problems using the s1, j1, or y1 cable tranny? I have heard that I will run into computer problems using this set up. Does it matter if I get a OBD 1 or OBD2 block? Which computer works best; Pr3, P72, or the Si ecu with a VTEC controller? Does anybody have experience with this set up? How reliable is it? Any help is greatly appreciated as well as opinions on how to build this up correctly. Thanks in advance.