Do I have a big problem??
 

I am in the process of getting my 89 GT ready for its new owner. I am attending school full time at UHA in CT, so I am only able to work on it every other weekend or so.

Last month it blew the intake gasket at the water passage. While it was sitting, the crankcase filled up with water. I replaced the gaskets and drained the crankcase completley. I put some new oil in the lifter valley to prelube the lifters, since that is where the water was gathering and then draining back to the crankcase. I also had water in the cylinders becuase I kept adding water until the rad was full, which meant the crankcase was full of water up to the cooling passage. Do you think the water washed the oil form the bearings? should I take the valve covers off and prelube the rocker arms? Do I have a big problem, or can i just fill it with oil and not worry about it?

If it were me i'd be more worried about the water that was in the cylinders if it sat in there for a long period of time.
Assuming you already cleared out as much water as possible and changed the oil and filter ... i'd run it for maybe 5 min without any load on it then change the oil and filter again.

If you want to pre lube it all you have to do is fill it with oil and borrow a prelube shaft from Autozome. This will assure oil is everywhere it needs to be prior to startup. THe cylinders are another story. If they sat full of water they may eat the rings in a few minutes but it'll take a teardown to see that, unless you have a borescope handy.

I got all of the water outta the cylinders right after it happened. I cranked it with the plugs out until it was clear. It was just sitting at the bottom of the oil pan for a while.

That engine flush stuff isnt a bad idea too, right before the oil change.