If you got the Flashpower housing, it has the correct length allen bolts. You say that you have cleaned out the bolt holes.
For antifreeze to leak out when just refilling, it would have such a massive crack that it would be visible. Just took the housing off my Hemi water pump housing. This is pretty simple, even for me. Thermostat, o-ring, housing fits into the o-ring perfectly, housing has a recess for thermostat, install the clamp housing and torque to 15-20 inch lbs. This housing is very simple. Believe you have something else going on. Take a closer look at everything.