Little update...

I pulled the intake off, and just as I thought, no water, the filter wasn't water soaked, the throttle body wasn't wet inside, nothing...
Went ahead and put the stock air box on, was getting tired of the deep sound from the short air intake.

I inspected all around, no burns, no lose wires. I pulled the plug wires from the plugs, they weren't wet, no water in the plug holes, so we can rule that out.

While I was under the hood, I disconnected the battery wire, and pulled the battery and IG1 fuse, to reset the ECU, let it sit like that for about 20 minutes.

Put about 2 gallons of gas in that I had from the garage for the lawn mower.

Got in the car, started it up. It didn't shake and idle rough like before, a little high, but the engine was cold, after a few minutes of running and me messing around under the hood, the idle dropped back down to around 700 rpm.

Took the car for a spin, ran a lot smoother, like I said before, it wasn't running rough. It did though, sputter out/bog down when putting my foot to the floor. I noticed it was 'cutting out' when it reached around 5000 rpm.

I'm going to tune it up tomorrow.

• Oil change
• Replace spark plugs with NGK Iridiums
• Replace spark plug wires
• Replace the distributor cap and rotor
• New tranny fluid
• Fuel filter

Let me know if I need anything else.

I also have two more questions. Does it matter if water is getting into the bell housing of the transmission? The flywheel cover does not sit flush with the engine, being as it has a little open groove on it, will water getting into there affect anything? Also, how to I check the valves? Someone told me to re-adjust the valve springs. I could not find anything in the Haynes manual, or online, other than I will need a feeler gauge.