Let's see if we can figure this out. You have an adapter plate that will bolt to your bell housing like the tranmission normally would. The upper bolts due thread into the bell housing and I believe they are 1/2 in. The lowers were a bolt with a nut. Drilling the t5 to 1/2 inch is done becuase the holes in the case are smaller (metric). This drilling should not be done on the bell housing, only on the transmission case.
It should all bolt together with the original bolts, with the exception that they will need to be a little longer because of the thickness of the adapter plate. Hope this helps.