RE: Patriot XL, smaller servos?
If I were building a Pat XL, I'd probably do exactly as you are proposing. All except the JR 331 servos. I've heard some bad things about the 331s and have stayed away from them. The JR 341s however are rock solid.
You probably realize that most "mini" servos nowadays have more torque and perform better than standard gear 25 years ago. As long as you pay attention to correct control horn geometry these servos will be fine. Side mounted to reduce drag--yes you should do it.
As for the custom battery pack, yes to that too. You can make it just about any shape you'd like.
Good ideas!