95 civic still won't start
 

I've posted this question before, and tried all of the suggestions with
no luck, so here I am again.

1995 Honda Civic LX, manual transmission, fuel injected, 150k mi

The engine was running rough this spring, so it was figured that one of
the cylinders wasn't firing. To test which was the dead cylinder, the
plug wires were pulled one at a time. Pulled #1 wire, engine died, #1
not the culprit. Put wire 1 back in, started engine back up, pulled #2
wire, engine died, #2 not the culprit. Put wire 2 back in, and the
engine never started again. Engine cranked over and over and over but
would not start. Didn't even try. Pulled engine, a valve was blown, put
in new valves, new rings, new alternator, new clutch, reinstalled
engine, all new fluids, all connections hooked up. Still, cranks
forever but does not start.

-All cylinders have compression.
-All plugs are firing.
-Fuel pump engages when key turned on.
-Cylinders are getting gas.
-Timing just reset to perfect

If my new alternator was bad, would that prevent the car from starting?
Is it possible my ECU is fried?
Is it possible there is fuel but no air coming in?
Would a bad ground prevent the car from starting?
Is it possible something else was fried when the plug wires were
pulled?

Pleeeeeeeease someone's gotta help me here, that Civic was my baby!