If you install the bolts without the thermostat housing in place they should go all the way in or nearly so.
If the distance between the bottom of the bolt head and the manifold with just the bolt installed is ( just numbers for example) 1/4" and the thermostat housing is 3/8" thick then the bolt bottoming is not the problem.
I would get some radiator fluorescent dye and see if your manifold has a pinhole or crack.