When you flush the ski the water runs in the reverse direction than when operating, hence the flush.
When the maintenance light flashed did you try to reset with the reset button on the handlebar? Routine maintenance light can be reset without throwing a code. If it will not reset, it's throwing a code and needs to be read.
You really need to find someone with a candoo pro or buds system to read the codes and determine what is actually malfunctioning before throwing money at temp sensor, knock sensor etc.
You should be turning 6900rpms at about 50-55mph. I'm just wondering if your TPS is out of range not allowing you ski to reach wot. A candoo pro or buds can diagnose that.
Good news about the pump, now just need to figure out this last problem.