Okay so i have a few issues I've been stumped with on my 98 eclipse rs (stock motor rebuild only 1400 miles old)

First when i dropped the motor i found that my master clutch cyl was completely junk, no pressure what so ever, I went to autozone and bought a new one for like 55 dollars or so.

Its about two months old and if i push the pedal slowly down it has no pressure and backs up into the resovoar < can't spell to save life. But if i push the pedal down fast and right from the top every time, it works great and holds its pressure.

Anyway i don't understand whats causing this because it never had an issue before the motor rebuild and i don't wanna rebuild it every month.

Question two, after the motor rebuild was done i noticed that when i torque the motor (1st to reverse) or anything that takes it one direction to the next quickly and sometimes not quickly i get a crackling cluck sound from the engine bay. i think it might be a motor mount but why and which one? (same bolts in same holes)

also i deleted the thermostat bypass (aka heater core) and removed the thermostat because the lines to the heater core cracked. is it bad to run it colder for too much longer (like 3 days old) and where can i find those lines, no auto store around here has them? (pre-bent lines from the metal ones back to the firewall).