Do you have a mark on the flywheel for TDC? If not, you need to mark it.
Assuming you do, it should be easy to check if the valves are close:
Pull off the valve cover so you can see the valves.
Turn the engine over (in the proper direction) to where the injector creaks, this should be about 20* before TDC.
Both valves should be closed.
Keep turning the engine, about 45* before BDC (bottom dead center) the exhaust valve should open.
Keep turning the engine, just before TDC the intake valve should open (there is some overlap where both valves are open)
Turn it just a little more, just after TDC the exhaust valve should close
Keep turning, about 15* after BDC the intake valve should close.
The engine should now be on compression stroke; the injector should fire again about 20* before TDC.
These numbers may not be exact for your engine, but you should be able to tell if the valve timing is way off or not. My guess is that it's way off.