First off never run an obd2 ecu if you don't have to, you don't have to so don't even consider it. Will the motor come with a engine harness? Even if is obd2 it will plug right up to the 94 civic harness. If you don't get the harness you can use your stock civic harness. You will need to rewire the alternator plug, distributor plugs, and injectors. There will be an extra sensor on the motor by the crank pulley that won't match anything on the 94 civic harness and can be disregarded. You can put the stock civic injectors in the 99 motor so you won't have to rewire, they also flow the same, 240cc's. The alternator is fairly straightforward: both style plugs have a blk/yel wire, orient them in the same relative position as each other and just match the other wires up with each other, both plugs will also have a wht/blu wire in the same relative position. Distribuutor can be a little tricky depending on the year. I usually figure them out in front of me so I don't want to give you bad instructions on that.

Sounds like you have all the mounts and everything figured out.