If the clutch is out then the thud is the engine turning over. Did you torque the headbolts down to 15ft/lbs each? Maybe take the head off and check the head gasket, if it's busted or torn then the engine can feel like it's impossible to start. Recently bought a motor which has a cracked head, it wouldn't start for nothing, cost me 50 bucks for the whole kit almost new, and it was an 8 dollar fix. Problem was he never torqued the head down, just let it go out of the factory box.
Look at head, and gasket, of they are messed up you'll need a new one of the broken, if nothings messed up, torque the head with a torque wrench, not by feel or by hand, to 15 foot pounds, there's a pattern to follow while tightening the head also