Ok, well I've gotten to work on it some. Based on what Hoser John said it don't look like it's the seal. I filled the pump with water, and covered the intake hole to see if it was leaking anywhere and it's not leaking.
It does have the big rubber o ring it looks to be in good shape, but a little flattened so I replaced it. I also cleaned the old silicone residue off it, and put some gasket former on the housing before I put it back together.
I'm back to thinking that I was just sucking air somewhere. Either around the housing from it not being put back on properly, or that intake hose. I'm not real thrilled with the intake hose either way, and it's been suspect #1 the whole time. I'm going to try to rig something up with it and go give it a try again here this evening. A few extra hose clamps and some water seal tape should eliminate and chance of that hose leaking air.
I'll post results later tonight.