I'm pretty much a newbie to fixing cars, and cars in general and am learning as I go, got a 96 Legacy just for this purpose. I'm still making all sorts of stupid mistakes, like this one:

96 Legacy, EJ22, 207k miles on it. Week ago, the crank bolt comes loose and harmonic balancer/crank pulley almost falls off. Make it home, spend the weekend fixing it (that timing sprocket was a BEAST to get off!!), get it back together, fill up the fluids and start driving the 60 miles to work. Sounded like a dream.

Within literally, 2 miles, the thermostat is pinned. I figured this might happen and had fluid with me just for such an event, but it happened so fast it caught me off guard. Filled it up, burped it, etc. Went on my way. Thermostat showed hotter than usual for another mile but as I pushed the engine up a hill, something (air bubble?) went and the needle dropped to normal where it stayed. 

Right after this, I start hearing a metallic tapping from the engine, mostly while idling at lights. Goes away as engine revs up. I'm running late for work so I dump 2 quarts of oil in there. Yes stupid. I know. But in the past few months I'd been leaking a lot more oil than usual, and it was the one thing I didn't check before leaving. Couldn't read any oil on the dipstick, so I dumped em in. 

Few miles later, tapping/knocking is happening more often, and after driving up a hill, engine starts surging in power, and stalling while idling. I limp into a parking lot, get a ride to work, and that night have the car towed home as it wouldn't even start.. 

I check it today, drain some of the oil back out, and after many many tries, it starts and runs really rough. Engine throws up 301 and 303 code. Spark plugs look okay, no oil in them, gaps okay, clean, etc. 

What did I do to my car?

 

Probably damaged the timing tensioner and its letting the belt flap around and skipped.

Pull the covers, check timing. Check the tensioner. Check any other parts you removed.

 

When refilling the cooling system on these cars you have to fill the engine through the upper radiator hose before filling the radiator. If you just fill the radiator, the engine is left empty because coolant can not get in past the thermostat.

Thanks for the tip on refilling the cooling system. 

I don't think it's the tensioner, I took several minutes to press it in with a C-clamp and held it in place with a pin, and with the belt, made sure all timing marks were lined up as close as can be (which seems to be half a tooth off of the pulley marks, it's either half a tooth, or 1.5 teeth off, so I went with the half), stared at it for a while and turned the engine several times to check, second-guessed myself, took the belt off and did it again, just to make sure). The belt is on tight, and drove for 5-10 miles without any issues. And the noises started gradually, and got worse, instead of all-of-a-sudden. Plus, if it was the timing belt, it would be affecting all cylinders, wouldn't it? Sometimes 1 &3 would be off, sometimes 2&4. Right?

No, timing can jump on only one cam and cause misfires on just those two cylinders.

The fact that it happened after driving could mean the tensioner was leaking oil and gradually got looser as you drove.

 

Check the timing.