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!
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fascion wrote:

you're standing at the passenger fender looking end on.
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jim beam wrote:

and rotor rotation is clockwise.
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Timing is on 100% correct.
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fascion wrote:

center. "firing sequence" is the order in which the plugs fire. if the plugs fire and fuel injects but it won't start, check the firing sequence.
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jim beam wrote:

and how did you check the timing if the motor won't run?
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jim beam wrote:

Well, I suppose I didn't "check" the timing, I just set it. When the distributor rotor was pointing to plug wire 1 ( bottom left ) the number one cylinder ( 4 3 2 1 ) was at top dead center. The belt was put on, and then tightened.
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It sounds like you are confusing valve timing and ignition timing. Valve timing is set by lining up the timing marks on the camshaft and crankshaft gears when the timing belt is installed. Ignition timing is when the spark occurs at the spark plug and is set with a timing light with the engine running.
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fascion wrote:

You have timing problems by the sounds of it.
As mentioned before, you have 'TWO' top dead centers on cylinder number one.
One is the compression stroke that you find by putting your finger in the spark plug hole and hand turning over the engine. When the crank pulley comes up to the 'timing mark', this will show compression under your finger. Setting it by the rotor just does not work.... You must use the timing marks.
The 'other' top dead center is when the exhaust valve is open so no compression will show under you finger. If you used this TDC, the engine won't run 'usually'
You also 'can' use a timing light to verify that you have it correct. The timing light will spark with just the starter turning things.
Mike 86/00 CJ7 Laredo, 33x9.5 BFG Muds, 'glass nose to tail in '00 88 Cherokee 235 BFG AT's Canadian Off Road Trips Photos: Non members can still view! Jan/06 http://www.imagestation.com/album/pictures.html?id !15147590 (More Off Road album links at bottom of the view page)
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fascion wrote:

not the cam belt timing. cam timing is important and it's vital it's set right, but the motor will run with cam timing a little out, same for ignition timing. it will /not/ run if the plugs are firing in the wrong order.
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until after the motor is running, an engine will run for quite some time on the battery alone

fry electronics, which you would not have created by pulling plugs

I'm not sure how you would do it in this model, but it may be worth checking for air flow. I cant think of any way that pulling a plug could permanently disable an engine, aside from creating a loose connection to the spark plug itself. This cant be what is happening if you are getting a spark though
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At least in Honda engines, opening a spark lead can zap the coil. My own experience in that is visible in http://tegger.com/hondafaq/badsecondary/internal-arcing.html (d'oh!) In that case there was no detectable spark, but the damage can be less so that a spark can be seen but it won't produce enough voltage to fire the plugs under compression. If the coil can produce a half inch spark that ought to do the job.
Mike
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Michael Pardee wrote:

component failure like this!
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fascion wrote:

When you pulled these ignition wires, what steps did you take to ensure that current from the ignition coil, which normally arcs across a sparkplug gap, has somewhere to go?
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