dont know much about hondas, anyway here are some common problems i know of people running into when swapping motors.
1. harness doesnt match the ecu, and vise versa
2. harness doesnt match the motor
3. poor wiring job, i dont know if you had to rewire the harness at all?
4. a fuse blows, a friend of mine spent $2k trying to figure out a problem on a similar motor when it turned out to be a fuse.
5. on nissans theres a little thing that tells the ecu to tell the injectors and plugs to fire, dont know if you have something like that but that could be the problem.

your problem is a simple one, if you have to hot wire the fuel pump then your wiring is bad, you've popped a fuse/relay, or you didnt plug in everything. good luck