Hydrolocked

I have a 2.4L Toyota vvti that will almost complete a 360 rotation but locks up between 350-360 degrees. It did suck up some water thru the intake but did not instantly die, it shut off after 1 or so after sucking up water. So my question is it more likely a valve train issue or the rotating assembly the cause? Is there a way to tell without pulling the engine? I did use a bore scope to view the valves and pistons but no visual signs of damage.

I would suggest to check the piston heights. There are a couple of ways to do this, but the quickest check would be to get either a really long 1/4in extension or piece of welding wire (any straight item that wont break off in the engine and fit down the spark plug hole but be long enough it will sit higher than the rocker cover even if the engine is at bottom dead centre)

It is a 2AZ-FE engine? If you put the piece of wire/rod down cylinder 3 and 3, they should be at the same height (you can mark your measuring device with a sharpie to the top of the spark plug tube for a point of comparison. This check can be completed on 1&4. No mater where in the travel the crank is, 2 and 3 should be the same height, and 1 and 4 should be the same height. If one is lower than its matching bore, then the chances are a rod has bent. If this is the case, I would be willing to bet that the reason the engine is locking up is the rod is catching the bottom of the bore as it is bent.

Excellent suggestion, Nathan.

+1 for bent rod, assuming no sign of a bent valve

May not be a problem with the bottom of the bore, but some engines (this one?) run the bottom of the skirt very close to the counterweights, and can interfere if the rod is compromised.