If you want to go to 35" tires I would recommend going with a YJ Spring Conversion instead of just a SPOA and lift springs. Your also going to want to pick up a set of Chromoly front axles, I think Trial Tough still has them on sale. When you install them you'll have to change your side gears out on the front diff. You will want the 6.5 or 8:1 transfer case to turn the wheels as well, unless you are going to do an engine swap. You might be better off switching to either Toyota or custom 9"/Dana 44 axles. Maybe a Coil Over from Trail Tough. I don't run into to many obstacles that need taller tires then the 33's on. I am stopped by the lack of wheelbase more often then clearance.
I have just a straight SPOA with Rear springs Up Front (RUF). With the 33" Pro Comp Xtreme Mud Terrains I have 19" of clearance to bottom of the frame. 1" lower then another club Sammy with 33 Swamper's with YJ Spring Over setup. To fit the tires i have
modified my front fenders for clearance. My rear fenders have also been cut out a few inches, but that was originally to get rid of rust.
If you do a search on SPOA you can find a few write ups on how they are done. There is nothing wrong with trying a 31" lift out on new tires first to see if you need to go taller. Unless you have a specific rig in mind that you want to build.
As for the flares, I run YJ front flares in the rear. Other people have modified the rear TJ Bushwacker flares to run on both front and back. There are quite a few ways to do it.