Below the upper pump case and impeller are two flat gaskets (one each side of the stainless guide plate), that come with the wp kit. Also, below the lower pump case, is an o-ring that seals the pump case to the LU housing, and two oil seals that seal the driveshaft as it enters the LU casting. If you are forced to heat the LU casting in an effort to get the corroded bolt stubs out, you will want to replace those (or at least pull them out of the LU casting) before applying any heat.
If you need to drill, try to get a left-hand-twist drill bit from the local industrial supply house. Sometimes, when the bit "bites", it will extract the bolt. It would also be a good idea to fabricate a drilling jig so that your bit stays centered on the hard bolt, rather than migrating (wandering) into the softer aluminum housing. OTOH, with a little heat, and some very careful use of vise grips on the remaining stubs, you may get the old bolts out without drilling at all. Once the bolts are out, chase the threads with a bottoming tap, and when you install the new bolts, apply a compound to provide a barrier between the dissimilar metals (stainless bolt, aluminum housing). That could be either "removable" lock-tite, or aluminum-based (not copper-based) anti-seize compound.