4runneroutlaw

So about two weeks ago I thought I'd be cool and go across a flooded creek...well long story short, bad idea.
My timing belt broke while I was out in the middle of it and pretty much everything got flooded.
I had my friend tow me home and I proceeded to tear into the engine (3.slow).
I replaced the timing belt and set the timing etc.
Flushed motor multiple times with new oil and added new K&N oil filter, also replaced intake gaskets and valve cover gaskets.
So now the motor starts and runs and all is well there and anyway I thought I was done and good to go...
Well I took off down the road and all was good for about 300 feet until the transmission quit doing anything at all...towed home again...
Apon inspection I noticed that my kickdown cable was loose at the transmission, in fact I can grab it about a foot and a half away from the throttle body and move it about 2 inches up or down and the cable kind of just bunches up at the throttle body instead of retracting back inside the tube...
Iv already drained the transmission fluid and am planning on taking the pan off and replacing the filter and pan gasket and putting fresh fluid in it.
Anyway my question is does the kick down cable have anything to do with it not pulling in any gear or do I have bigger problems??