If you did a compression test and got 30psi on any cylinder go ahead and take the head back off.
When you set timing with the head off the block, you turn the crank clockwise and watch cylinder #1, which is the pass side cylinder on your car. When that piston comes up to the top, that's TDC.
You don't need to worry about the flywheel, as long as the crank pulley and cam pulley line up to their marks before AND after you put a timing belt on, you should be golden.
So, if this what you did, and are positive you had everything done right, you might have coincidentally broken either the cam pulley key way or the crank pulley key way.