1995 Honda Civic Engine knocking, failure to start

Okay, for starters, this past weekend, the internal water pump(timing belt driven) wore out from overheating due to a faulty thermostat. Although I realize the damage was most likely worsened, I had no choice but to drive it in intervals of 4 miles for 45 miles back to town (lack of funds for towing). So I replaced the water pump, thermostat, and timing belt. It ran and sounded great after all said and done. Sat and idled smoothly for twenty minutes with no overheating or odd sounds. After driving only a short distance (<20 miles) around town, a light knocking from the engine began to ring out, but only when idling or at low speeds (25mph). In four days with no luck of locating the source, the knocking progressively became louder, acceleration became sluggish, and idle in P, R, N, and D dropped to avg around 500 rpm's. Thinking it was a timing issue, I loosened the bolts on the distributor and adjusted it slightly while the engine was running. After locating the best position by sound, I tightened it back and the engine idled down and died. Since then, it will not start. The engine cranks with no odd sounds, there is spark, replaced fuel filter, but still no start. Any ideas?