Apparently there’s a little timing control module in the ecu that CAN, in rare circumstances, go bad.
As for exhaust restrictions, I’ve been down that route…I checked it again by pulling the upstream o2 plug and cranking her. No dice.
Did a quick switch back to the old ECU (and pulled out the accompanying key) and tried again, still nothing.
I’ve got spark, fuel, compression. And no exhaust restriction. And no idea.
Cheap… bout 25-30 bucks… Of course do your normal spark checks first… If you have a yellow or orange spark…its the ignitor… If you have no spark…it will be hall sensor in distributor or the ignition coil… These all test and rule out quickly if you are used to it.
You have to tell us tho… Whatchagots?
Most accord no starts are the PGM/Fi relay…or the distributor…and more specifically the ignitor. Coils are pretty solid and dont eff up much…but that ignitor? It goes on more vacations than Paris Hilton.
But if your plugs are being drowned by fuel…which seems likely…you either have no spark or insuficient spark energy (Ignitor). You need to test and tell us…what color is your spark? IF you have spark…
Helps to have the “Accord No Start Kit” that I have on hand constantly… it consists of a full distributor… An new known good ignitor, a new Known good Ignition coil and a new known good PGM/Fi relay.
Out of the last 100 or so Accords Ive gotten running again…one of those items in my kit did it…sometimes two parts… Then I remove mine…and install new ones for the customer so the known good goods stay in my kit… LOL Havent failed me yet… But theres time for that…
Blackbird
Just before this car was set aside for awhile, was the timing belt changed? Do you know when the timing belt was last changed? Have your removed the valve cover and the upper timing belt cover to see if the timing belt has stretched and maybe jumped a tooth or two?
If the timing was off on a Honda, I would suspect the timing belt before I would replace the ECU.
Oh hell yes… Are we suspecting a timing jump ? There are ways to check for this…and they do not take long.
Hard to advise remotely like this… Like I always say…I can do 10 rapid fire checks in minutes literally… that take days here on the forum. Sometimes…often actually…you can smell the problem.
I dont have Smellavision here so that option is out…
Blackbird
Checked for timing belt jump already 
T Belt on this car is overdue for a change. But not she’s working again!
Interesting points from blackbird; I do have spark at all 4 ignition wires. I don’t think my tester tells me how strong that spark is. (Just a probe with a vacuum tube(?) that lights up) I can tell you it really hurts, though! But maybe I need something that gives me a more exact reading of how hot the spark is?
Considering calling a scrapyard to find a compatible distributor just to see what happens if I swap…
Pull the plugs, and let the cylinders air out over night. Try again tomorrow morning.
From what I can see the ignition timing is not shop adjustable on a 99 Accord w/a L4-2254cc 2.3L engine. The timing is entirely determined by the ECM. It’s supposed to be 12 deg BTDC with the engine idling, and warmed up. Make sure it’s idled long enough the radiator fan has come on, that means it is warmed up sufficiently. OP should verify the timing with a timing light hooked to the number 1 spark plug wire, aiming at the timing wheel. Apparently there’s a red mark there indicating 12 deg BTDC.
Note that it may be required to set the ECM into a special test mode to measure timing accurately. That would be done by the scan tool. Honda’s own scan tool can definitely do this. Not sure about the aftermarket versions.
It’s not possible to warm the engine up if it won’t start obviously, but it is still possible to check ignition timing during cranking to get an approximate reading. It should still measure in that 12 deg range.
If an ignition timing problem is suspected, my first guess would be a faulty crank position sensor. That’s how the ECM determines the basic engine timing.
Possibly an informative story: Years ago I owned a VW Rabbit. A mechanical fuel injection system that tended to clog w/grit from bad gas. After testing the fuel injection system for an idling problem, when I put everything back together the engine wouldn’t start. Not matter what I did, it wouldn’t start. I put a spark plug on each spark wire one by one, held it against the chasis, excellent spark on all. Checked the timing with a timing light during cranking on all four spark plugs, looked good. Fuel pressure, fine. No indications of sensor, valve, air intake, or exhaust problems. Compression fine in all 4 cylinders. I had good fuel, good spark, good timing, good cranking. Still wouldn’t start. After a couple days of frustrating trying this, trying that I discovered the spark plug electrodes were coated with fuel. It turned out that the tests I had done on the fuel injection system had pumped a lot of gasoline into the cylinders. And I mean a lot. The solution to get it to start was easy. Remove the spark plugs, crank the engine a few times, and let the gasoline slowly evaporate from the cylinders. Took a couple of days, then installed the spark plugs, it started right up and ran like new.
Alright, I’ll try leaving the spark plugs out overnight. We’ll see how it goes tomorrow.
If nothing, I’ll dig around for my timing light and see what I can do there.
I’ve also ordered an adapter for my fuel pressure test kit to fit this Honda. Won’t be here for a few days though.
To heck with the timing light… While you have the plugs out…hook one up to the wires the proper wire and have a buddy or use appropriate tools to turn engine over.
WHAT COLOR IS YOUR SPARK? Blue/White = Good… Yellow/Orange = POOP
When Blue White…it will be audible as well as visual… Trust me there is a difference
I’ve been hit with Ignition Voltage so many times I could tell you the color from the level of pain induced… Hahaha… NO I don’t recommend this method but I’m not joking. Blue White will tick you off so much you’ll want to slap your Momma which is shocking to say the least ! I could take Yellow Orange on my tongue…LOL
I believe the Ignitor is some sort of high voltage amplifier… Not sure why they incorporated this but they have become common. When the ignitor fails…you have spark…just not strong enough…which I know…IS Confusing.
Again…simple test
Blackbird
Well this is interesting…Put the new ECU back in and got the appropriate key, and went to check spark. And there is no spark. Not at the wires or the distributor. Double checked all the connections and the ignition fuse.
Blackbird, to try and answer your question as well. I was going to use a screwdriver today to observe the spark directly, but yesterday I used my pen-type spark tester, which just re-creates the spark in a glass tube in the “pen”. That spark was yellow-orange, for what it’s worth.
Chagned back too the old (original) ECU, tried again at all 4 cylinders, cranking a full second or so on each one. Got a total of 2 (orange) sparks. Ok, looks like there’s a problem here.
It’s worth mentioning that this car is outside, and yesterday was really bright sunlight. It was all I could do to make out the spark at all. I’m not sure how often it was firing. Today is overcast I can see it clearly.
Check the cap and rotor. There will be 4 little electrical contacts in the cap which the rotor connects with to send electricity to the spark plugs. If they’re worn or fouled they can stop the spark plugs from getting the electricity.
If that looks good then it is time to start looking at the coil and igniter.
Thanks. Apparently I can test the coil and igniter but I need a tester that goes to ground first. Will put in an order for that.
Ignitor… Inside the distributor…two phillips screws and about 15 minutes
@“Mike Wretzel”
this is what you use to check for that extremely blue spark
http://www.napaonline.com/napa/en/p/BK_7002456
simple to use, and sure beats using a screwdriver or your tongue 
“your tongue” ?? what a strange, and very dangerous, idea.
The Tongue Test only comes out when there are drunk hecklers in or near the diagnosis site… HAHAHA
Dangerous ? Don’t even get me started on the things I could list… That was one of the milder ones… All in good fun.
What you havent Tazered your buddies yet ? Oh Jeez…the mayhem Ive lived through.
Blackbird