Wrxxin

Ok, so I've got an 03 wrx with a few mods (turbo back 3" exhaust, catless up pipe, act streetlight flywheel, cold air intake, Cobb tuned stage 1...) and I have 2 separate noises coming from the trans/clutch. The car has just under 80k on it, and this is the second trans and clutch. The previous owner beat on it a bit. At about 60k 2nd gear took a dump so I put a used trans in it ( I know awful idea, but hey times were tight) and a new clutch. It all started when I went to pull out from my street and didn't realize I was in second gear still. I stalled due to letting the clutch out too quickly. So I started it back up and went to drive off. Once I shifted it into 2nd gear I got a rhythmic clicking related to the speed. It also makes the noise in 4th and reverse, but not in 1st, 3rd, or 5th. Not only that, but now when the car is in neutral and the clutch pedal is out I have a rhythmic clicking related to the engine rpm. The second noise I assume is the throwout bearing. I'd love to avoid replacing the transmission, I'm pretty sure it's something to do with the shifter or synchro or something since I didn't stall in 4th or reverse. If anyone could point me in the right direction it would be hugely appreciated. Let me know if any other info could help, thanks!