Having the pumps that close to the engine compartments exposes them to a lot of heat. Would recommend running the directly off the bag. The aerator pumps have a difficult time draining bags because they do not self prime. Once they loose the prime it is difficult to get them going again. If your bags are not vented properly and you are getting air pockets this will also cause problems. Try stepping on the bag to force water into the pump, usually once you get a prime it will start to drain out. Also might want to check for any debris that could be caught up inside the pump area.

If I ever add pumps again they will be Impeller driven, they self prime and will remove all the water out of the bags. They have been getting really good reviews from '09 and later Supra/Moomba owners. Only downfall to them is they can toast impellers if ran dry. For $100 extra per pump you can get timers for them to eliminate this from happening. They are more expensive but are simple and require no vented loops, and drain and fill out the same port.