98 Civic 5 speed D16y7 won't run
 

I'm trying to help my son get his Civic up and running.Since I don't have a FSM for it (I even tried to download 1, but failed), I'm kind of blind to what I should trouble shoot. Currently, it'll turn over, but has no spark, no fuel pump, and no CEL light (doesn't turn on at all). But, if you use a test light, you can get the fuel pump to energize, so we know it's good. We checked all fuses with an ohm meter, and they're all good. Swapped out the main relay for a known good one...nothing. I even put a code scanner on it, to see if it would cough up a code, but the scanner is acting like there's no computer to communicate with (might have something to do with no CEL light?). We checked and cleaned ALL underhood grounds to. Nothing changed.

The engine had just been rebuilt, but hasn't fired off yet. The car did run before, but had a rod knock (#4) and was removed for rebuilding (was driven into the garage, then engine pulled, then pushed outside). We dropped the rebuilt engine in, and now we have basically nothing, other than the starter turning it over. Any ideas?? To me it's acting like something isn't getting power or communicating with everything else. But I don't know what's lacking, as I don't have a trouble shooting page/section for it.
Thanks for ANY help you can offer.

Most likely some wires/connections.. back track..

We did that too, as my first thought was something wasn't plugged in. Then we checked the grounds as I know Honda has some that won't let the car run if left unplugged (I own an Accord).

Any idea on what actually powers up the main relay? We did check the fuses (all were good), but that doesn't help me when I don't know what actually powers it up. I only say that because the main relay has power in places but not all, as I can use a test light on the fuel pump terminal of it, and it'll bring on the pump (otherwise it's off). But it acts more like the ECU isn't powering up, due to no CEL light on (or my scanner not recognizing the ECU).

We did finally get a FSM (late last week) so I could do a "pin out" test of the ECU (over the weekend), and found no ground for LG1, LG2, PG1, and PG2. These all go to G101 at the thermostat. And while the connection was clean and tight, the wires inside the plastic sleeve were broke. Got that fixed and then replaced the burned out MIL bulb (why we didn't have a CEL light). However it still wouldn't run, so we swapped in a "known good" ECM/PCM according to the FSM trouble shooting, and it fired right up. So it was a combination of things that kept it from running.