I prefer stock so that you can install the lift you want and know it's done properly. However, if wife is saying NO to doing it yourself, then get one with a good lift - make sure it has all the required suspension modifications to keep suspension and steering geometry correct (e.g. adj trackbars, adj control arms, brackets, extended brake lines, bump stops, longer sway bar links, etc.). All too often, dealers just lift a Jeep to make it look good sitting on the lot, but don't take these things into consideration.
rubi with miles, or x with less?
If you want lockers and D44 axles, Rubicon's the way to go. Especially if the wife doesn't want you to build up a Jeep. A D44 will hold up to 35s much better than a D30. Miles are no big deal. Besides, if the engine goes, swap it with a Hemi!
will a manual tranny keep up with 35" tires and towing?
Absolutely. Manual transmission is the way to go. I have 35s on stock Rubi gears and have been perfectly satisfied. I've towed small stuff (<2,000lbs) like small boats, PWCs, etc. and haven't had any trouble.
will the automatic be a better option?
No. See above comment. If you get an automatic with 35s, you will want to re-gear. Some programmers will help with adjusting shift points and getting the powerband better aligned with shift points, but re-gearing will eventually happen. Besides, I find autos boring, but that's a personal choice.
can i live with no power options?
You can live without power options, but it's nice to have power windows for the rear doors - especially with small kids. If you get the Rubicon model, I think it comes with all the power options (windows and locks).
Seems like you generally know what you are looking for, just need to find it. Be patient and don't make an emotional purchase. There are plenty of good used JKs out there. Spend some time on the forums and learn about what to look for in a lift and what questions to ask the dealer.
Also, don't be afraid to take pictures of the undercarriage and lift components with your cell phone and post them up here for comments. I've seen that happen a time or two. Let us help. Good luck.