so Im replacing the upper intake, it flooded the engine and I need to get the water out of the cylinders so I unplugged the fuel pump relay and went to crank it with the spark plugs removed and the upper intake off, but now they starter wont crank, it whirs like its engaged, put it sounds like it isn't meshing with the flywheel, are the pull in windings tied into the fuel pump relay somehow, or is something possibly unplugged, I checked the starter and everything seems to be good there or at least all the wires are still attached to it, not sure what is causing it to not mesh, please help, I don't have access to a shop vac to just suck the fluid out, so this was the only way I could think of

That is the pretty much the proper way to clear the cylinders is by removing all of the sparkplugs.

You may have damaged the starter or flywheel by maybe trying to start it while it was still hydrolocked?

i would guess that too, take the starter out and inspect the fly wheel and the starter gear. you can try the starter on the floor and make sure the gear comes all the way out

There is a solenoid that piggy backs on the starter. The solenoid drives the starter gear forward to engage the ring gear on the flywheel. If the starter is turning but not engaging it could one of three things; the gear on the starter is broken, the gear on the flywheel is broken, or the solenoid is not working. Take the starter off and inspect the gear on the starter. Using a set of jumper cables apply 12 volts to the terminals on the starter and observe if the solenoid moves the gear forward as it spins. Using a wrench on the bolt that secures the harmonic balancer to the crankshaft, turn the motor over bit by bit so you can inspect the ring gear on the flywheel.

This should lead to the problem.

In the mean time you should be able to crank the engine over by hand, especially with the spark plugs out. Just throw a socket/ratchet on the harmonic balancer and crank it around.