You may have no choice other than drilling them out. If the holes are threaded, there is a good chance You will have to Helicoil them.
In spite of having a little chunk of zinc or magnesium on the cavitation plate for galvanic protection, the combination of aluminum in contact with stainless becomes a galvanic cell when wet with an electrolite [salt or brackish water]. This causes the corosion that binds the bolts into the holes.
When You reassemble the motor You need to use Lock Tight or Teff Gell to reduce the chances of galvanic corosion.
This applies to all hardware that is bolted to Your aluminum bolt. In addition, any metals other than aluminum need to be seperated from the aluminum with an insulating spacer [plastic].
The best method is to use plastic spacers and washers and thin plastic tube around the bolt to eliminate contact with less noble metals.
Never Sieze will not do the job.
Hello Chris, you may need to go the route that Dave suggested. However, before you consider only that you may wish to try using the GTAW process and some stainless filler rod. In the "tricks of the trade" section there are a few threads where folks have included tricks for using welding as an option for sheared/broken bolts/taps/etc. I like GTAW for my removal tool on broken items providing that they aren't too deeply broken off or too small, although I have removed broken machine screws as small as 4-40's with that method.
Since you have aluminum as the base material and it doesn't readily combine with the stainless when you are welding on the stainless portion there is a certain amount of safety from damaging the aluminum. Clean the area with your stainless wire brush as well as possible and then start applying small stainless beads around the outer perimeter of the broken stainless bolt and spiral into the center of the broken bolt. Continue to do this in layers until you can grip the built-up portion with vise-grips or other suitable type tools. You can also weld and build-up in a similar fashion and incorporate a washer into the welding process and then weld a nut to the washer and then use a wrench to back-out the broken bolt. However you build-up and grip the broken portion, the heat from this welding will generally aid in breaking the bolt free and with a bit of lube(paraffin or bees wax melted onto the area after welding, aerokroil, WD-40, PB Blaster, or other lubricants) by working the broken bolt back and forth and having a bit of patience you will generally be able to safely remove the broken piece.
I'll see if I can find some of the examples of this and include them here to give you an idea. Good luck and best regards, Allan