Is $2,000 to turn a green pool around and fix flow issues a fair price?

My old pool pump broke about a year and a half ago. The original plumbing to the pump and filter had been cut, and someone tried to install a very small pool pump meant for an above-ground pool. I got a new pump and reconnected the plumbing, but the pool and spa are still green. I've been shocking, treating, and scrubbing for about a month, and while there's no new algae growth, there's about an inch of dead algae on the bottom that I'm slowly vacuuming out. I'm struggling with flow issues, as the main drain isn't sucking even when I sweep, and the spa doesn't fill if I close the skimmer valve. My chlorine levels are a bit low, and pH is on the underside. I don't have a lot of money for this project.