Short summary of sequence of events:

Purchased 2000 SR5 MT about a month ago with aftermarket air intake that I think there may be a small vacuum leak in.

No issues presented until this week with fluctuating RPMS and rough idle accompanied by a misfire in cylinder 4. Engine would randomly rev itself.

Cleaned the MAF and throttle body and now fluctuating rpms seem to be fixed, MAF was covered in buildup.

Changed the cylinder 4 spark plug too and am waiting on wires to come in the mail along with the rest of the spark plugs.

Now there is an abnormally low idle (a little below 500rpm) and still a misfire in cylinder 4 but I also got an additional multiple cylinder misfire code (P0300). Misfires go away after barely kissing the throttle and holding it (around 1000 rpm in neutral, hard to hold it lower).

After swapping the wires when they get here, is redoing the vacuum hosing the next logical step? What else could cause the low idle? I know it's cheapest to buy in bulk but what sizes are needed?

I'm hoping to replace the air intake and filter back to stock but am unsure of the part numbers to buy as it seems there are two boxes with the stock air intake? I currently have an aftermarket spectre intake but would appreciate if anyone knew the part numbers to look for.

EDIT: Swapped Plugs and Wires for Denso and NGK. Misfire gone. Car still starts out with normal idle (~800rpm) which then drops to a low idle ~500rpm or even dipping into the 400s. When clutch is depressed, RPMS dive all the way to low idle much faster than usual, so the rpms kind of bounce around when shifting if I'm not right on the money, requiring a lot more throttle control when shifting. Some lurching transitions and acceleration as I let off the clutch. Fuel filter or vacuum leak causing lack of power?

Mostly 3 things: Ignition, fuel or head gaskets. My signature has the factory spec reading for the coils and wires. Fuel would be not enough pressure or plugged injectors and the head gasket can be checked with what they call a leak-down test.

So this is unlikely to be caused by a vacuum leak? Also, suspicious that my valve cover gasket on the same side as the misfire may be leaking so wondering if that could cause it too. Planning on swapping the PCV valve too since its gunked up and greasy on the outside.

If it's more likely fuel related, would the fuel filter be a good place to start? There's definitely something wrong with that system as I have an EVAP leak and can smell gasoline pretty strong when filling up.

Probably not a vacuum leak. Test the coil too by swapping cylinders, if the miss is on cylinder 4, move its corresponding coil from cylinder 1 to 3 or 5. If misfire follows you have a bad coil. The test is free.

Planning on doing that when I swap the plugs today. Hopefully this turns out alright. Also planning on changing the fuel filter to see if that helps anything since I have no idea if the previous owner replaced it.

After replacing the wires, don't throw any more parts at it before you do some more diagnosing.

I recommend a compression test followed by a leak-down test of any cylinders showing low compression.

I have videos for both jobs.

Engine Compression Test - Timmy the Toolman

Engine Cylinder Leak Down Test - Timmy the Toolman

Glade you were able to fix the issue. For the low idle, I'd say clean the throttle body and IAC if you have not done already. The low rpm could be a sticking iac (idle control valve). But also check for vacuum leaks. Check all small vacuum hoses too.