Now, my fear is about the possibility of a bent valve. After I applied some force on the ratchet with an extension (while trying to turn the cam to tdc while the crank was already at tdc), I had to change the shim on the exhaust on the #4 piston. The previously measured clearance was .017 then after it was .025. So I changed the shim and everything seems to be working fine, but should I opend the head to check before I refit the engine in the car? Is there another way to check?
If the clearance changed after you applied force...
I really really hope I'm wrong, but I'd be betting nine chances out of ten that the valve is bent. (the tenth chance is that the .017 was measured with the cam lobe not quite in position, or something more unlikely).
Do not put the engine back in the car until you've resolved this. It's all just so much easier to do this stuff on the bench.
You can do a leak down test, see if the valve is still sealing properly. I'd do that before I pulled the head, but I already have the air compressor and a cheapie leak down tester from Harbor Freight.