Fever32

I have a 97 Fountain Fever with twin 502's that's new to me. I winterized it myself for the first time this year using the freshwater flush. This was a bad idea since I didn't do it under pressure; I just sucked the AF out of the jug using a hose. So I burned up my lower water pump impellers on both motors. I replaced them today and cleaned all of the rubber pieces out of the coolers. But now when I start the motor I can only get water to come out of the exhaust thru the transom, when its hooked up with a garden hose using the fresh water flush. When I turn the flush off, it isn't sucking water into the water pump through the lower unit. I only tried the STBD motor because I was pressed for time. I'm sure its something obvious, but this is the first boat I've owned with a fresh water flush. Any suggestions? Thanks!