I will suggest getting everything from a Y7, axles, harness, ecu, etc. It should fit ok. You guys must've done something wrong in your bros car.
Although I concur you must have done something wrong...I don't see how y7 axles are going to help. I assume you're running the stock L3 tranny? Use whatever axles were meant for your car.
And you sure as hell don't want the obd-2 ecu
First off, what kind of 89 Civic...MPFI or DPFI? You're not giving us very much to go on.
For the 96-00 D-series motors into a 88-91 Civic, I understand you have to switch driver side motor mounts/bracket. Don't ask me which way...it's the y7 or the a6...one of them works
If you've got MPFI already, all those components(intake manifold, distributor etc bolt onto a y8...Maybe, likely, the y7 is the same.
Try looking at the y7 bare block/head as a self contained unit.
Now attach everything from your D16a6 MPFI to the y7 head/block. Take the A6 wiring harness, figure out what plug goes where. At least 90% of them will plug in because you're using as many A6 parts as possible. There may be a few plugs on the y7 block that require changing the A6 plugs to fit the y7 fittings(something about the coolant fan switch comes to mind).
IF you can get an a6 ecu wired to all it's necessary components, and those components are attached to y7 block/head, it should run just like a a6.