Dealing with rusty bolts

WD-40 is a water displacement product, not a penetrant or an anti-sieze. PB Blaster is a very good penetrant, and either the copper-based or graphite-based anti-sieze are well advised. If you are threading through water passages consider wrapping the thread-ends with Teflon tape to keep the hot, pressurized water from subbing up the threads and causing other issues (similar to through-bolts on crankshaft-to-flywheel flanges).