Ryan,
I previously had some of the problems you describe. I had to resort to using a Floccing agent to get the dead algae/particles to cling to each other and fall to the bottom, making it easy to vacuum them out of the pool. One year, the water was so bad (we had a tree overhead and winter cover sprung a leak), the water looked as thick as playdough! I shocked constantly, and used a gallon of algaecide by the time i was done. The process took about a week. From totally green, pasty-looking to cloudy to finally clear. What i found out that year was it was best to vacuum to clumps off the bottom and out of the pool rather than recycling the water. I eventually needed about 3-4 more inches of water, but it was the Floc that worked for me. I then kept a bottle of Floc on hand.