I feel badly for both of your kitties! Your tom cat is behaving normally. Has he been neutered?? I'm going to suggest you check out Jackson Galaxys Spirit Essences
http://www.spiritessences.com . He has a product for bulling and products for other behavior. Your bengal is completely STRESSED out over the bullying. Can you blame her? I don't think the solution is to rehome or euthanize your tom cat that you've had for years. You obviously did not introduce them properly in the beginning by separating the bengal in a "safe room" and doing swap scents for several days.
I am happy to hear there has been a truce, but the inappropriate peeing is not going to stop. You can thank your wife for showing the tom cat how to get into the cat run. You definitely should have a cat tree for your bengal, and 3 litter boxes. You may need to catify your home a little more, too! A cat whisperer is probably not going to help. I'd also buy some Feliway plugs and use them in the rooms the cats use. I honestly don't blame the female. She's feeling the stress you're feeling as well. I think she's overwhelmed. The cat run was HER place. I'd give it back to her and do something else for your tom cat. You should also be engaging the kitties in lots of play time. Bengals are very social and need the interaction with humans. Your tom cat may not. You cannot just let the cats try to sort things out. It won't happen! Intervene and follow our suggestions and things should improve.
Good luck and keep us informed!