Subie clicking from crankshaft?

My boyfriend has 95 subaru legacy L 2.2 that has issues.
NEW: coil pack, fuel pump, spark plugs n wires, battery. (I forget the rest)

Backround: While running the car almost out of gas (as usual) it starts to run rough, just thinking it was the gas, he gets gas and heads home but it does not fix the roughness. It stalls in driveway (lucky). A friend brings over obd scanner. Reads codes for cylinder 1&4 misfire. It starts and runs but sounds like ****. I tested the coil pack and the reading was bad, so got that and sparks n wires. Cleaned a bunch of fuel related parts (sorry on specifics here its been a while) and took out injector but apparently it was not back in all the way because fuel came spray/flooding out while another friend had a sparkplug out and was testing it for spark!! (luckily he was not harmed) After this it has not started. We did get the injector back in all the way, and waited to work on it figuring it was flooded and that time would help. Next was the fuel pump, yay i can hear it now, boo still didnt help. Now car clicks. Ok, starter out, tested THREE times at advance auto, and once at napa. They both say it is good. (I have my doubts though, it sounded slow to start up to me). Battery is also tested, bad cell. Checked flywheel, Put starter back in and new battery with 625 cold crankin amps. Car cranks now, but no start. Clicking noise when crankshaft turns.

Q: Do you guys think the engine is still flooded?
Q: Did the flooding foul the new spark plugs?
Q: WHY is the crankshaft clicking?
Q: WHERE is the nearest cliff?

Thanks in advance to anyone who is willing to help us out!

You might be better off if you just have a professional mechanic work on your cars from now on…

I doubt that it is still flooded. You can remove the plugs and turn it over a few times to clear it. You need to see if you have spark or any codes listed. Really you should not just pull plugs and see if they spark with out a plug tester. This can damage the ignition system.

It happening while running out of gas, I’d be inclined to look at the fuel supply first. Maybe it sucked some sludge from the bottom of the tank and it clogged some of the injectors. I’d swap the injectors with some in the non-misfiring injectors to see if the problem wants to travel. Not sure what the clicking from the crank shaft would be. Maybe the solenoid on the starter doesn’t retract the starter’s gear completely and it touches the flywheel slightly. I’d make sure that the starter operates correctly.

You could try (carefully) seeing if it will start briefly with a can of starting fluid. If it does, you know you have a fuel problem. If you have both spark and fuel and it won’t start, the problem could be that the timing belt jumped.

hmmm … well, it sounds like it’s cranking robustly, that’s a good sign at least. I’m assuming all the drive train fluid levels are fresh & up to spec, esp the crankcase oil. I think the missing DTC’s may have been from the time it ran out of gas, that will cause lean conditions and missing. Lean mixtures can also cause overheating, so that’s a bit of a worry, may be related to the clicking noise you are hearing. But a little clicking shouldn’t prevent the engine from starting, unless it is the timing belt/chain that has broke. Good idea to double check that is intact.

I guess if this were my car and I thought it might be flooded I’d disable the fuel pump, hook up a fuel pressure guage to the injector rail, and remove all the spark plugs and crank the engine a few times until the fuel pressure reads zero, then let it sit overnight with the spark plugs out, so any remaining fuel in the cylinders can evaporate. Then I’d reinstall the spark plugs (assuming they look ok, no unusual deposits, the electrodes look good, and are gapped correctly), repressurize the fuel rail, and measure the fuel pressure during cranking. I expect you’ll see a problem with that reading, as mentioned by @RemcoW, the fuel pump may have sucked some debris and it is clogging the pump screen or the fuel filter.

If not, then it is on to the spark and spark timing. If it isn’t an ignition problem, then measure the compression. If not that, about the only thing left is valve timing.

If it’s flooded, you will normally smell gas while cranking. To clear a flooded condition, just hold the accelerator to the floor while cranking–the ECM is programmed to feed no fuel in such a situation to clear floods, somewhat mimicking what you would do to start a flooded carbureted engine.