I replaced head gasket, intake manifold gasket, injector o-rings, worn hoses and vacuum lines, PCV valve, cap, rotor, spark plugs. Followed procedure in manual for replacing timing belt. Belt looked fine on inspection. I have done this before without problem.
Car started and idled but died when I tried to give it gas. Tried again and would sputter then die.
I rechecked the timing belt and crank pulley and cam pulley were both at TDC simultaneousy. Fine. Checked for spark at all 4 plugs. Fine. Also tested coil and ignighter. Fine.
I loosened the fuel line at the fuel bar. Gas squirts out when key is turned on. I can 't be sure it has the proper pressure but it is getting fuel to the gas bar.
Tried to start car it started immediately and idled for 3 or 4 seconds. It sounded totally normal then it died and I tried to restart but couldn't fire. It felt like it ran out of gas or someone turned the key off. It has done this numerous times. Starts right up, sounds nornal then dies.
I have just replaced the main injector relay. I am still having the same problem.

Has anyone seen anything like this, Electrical, Fuel pump, some intake sensor?

I did everything you did, plus some more, to a 2002 Civic several weeks ago. When I finished, it ran great for several hours and then refused to start. I replaced the igniter and coil and it fired right up and has been running ever since. You may have spark and it's firing, but not when the ECM needs it to. My experience has been that bench testing igniters and coils is a waste of time. Instead, I recommend replacing them every 120,000 miles or 10 years, whichever comes first.