Could be a ton of different things. At this point if you want to keep it might as well tear it down and build up with better parts at the weak points (pistons, rods, bearings). Could be something less, but why risk the extra trouble of not knowing what you have? Sorry you have had so much trouble, it comes with the territory when buying high mileage items that have a lot of wear. That said- a 2000 2.5RS with a 2.5l WRX engine is an awesome ride. The real problem is that if you didn't swap the transmission you will have a grenade on your hands. Trust me, I'm on transmission #3, where I finally had one built with PPG gears and a front LSD.
Best of luck with getting things fixed.