I have a 94 Honda Civic. It would crank but not start, I jumped terminal 5 and 7, on the main relay and fuel pump would kick on, got a replacement relay form Honda fuel pump still does not come on, other then the relay being bad is there any thing I am missing that could be the problem.

 

First carefully inspect the main relay connector and its associated wires for damage or corrosion.

With the ignition key ON, next check whether terminal 1 is receiving battery voltage and, if so, whether terminal 3 has battery voltage that is being sent to ECU terminals A25 and B1. Also check for inappropriate lack of continuity from terminal 2 to ground. You might have an open wire in one of these circuits.

 

checked all I show voltage from 1-3, and 1-2. but nothing from 2-3.
car does have an aftermarket alarm, but has not been used since I cot the gar from my sister about 4 years ago,

 

To clarify, are you doing the multimeter tests on the main relay connector disconnected from the main relay?

In this case, do you measure battery voltage when you touch terminal 5 to terminal 2 only with the ignition key turned to ON? Also do you measure battery voltage when you touch terminal 1 to terminal 8 without the ignition key turned ON?

Do you know how the alarm is wired into the system?

You probably need to do the troubleshooting described on the second page of the diagrams below:

 

I ran through the entire flow chart, everthing says good, is it the ecu or other problem.

 

Not sure what you mean by "other problem", but if I understand correctly, the tests point to a bad ECU, which is rare but not unheard of.