To answer the first question, yes the 2.5" springs on top of the axles will fit a 38.5" tire. You will either have to put the body lift on or get the saw after the fenders though, because it will still rub in the front and back when it flexes.
You will have to address many other problems: Your stock axles with these tires won't be wide enough to turn the tire without hitting the springs. Even the 14.50 Bogger will rub. Your gearing is going to have to change to get the power back...probably have to go to a 5.13. The stock power steering (even with high steer) doesn't like to turn that big a tire. It will be fine on the road but very difficult on the trails. You will also have to add traction bars to the rear if you do the spring over, because when the Boggers grab solid ground they either go or break something.
All of this is pending how hard you wheel your Jeep, but as a general rule I would max the stock axles out with 33's. A Dana 44 or similar can handle a 35" bogger or 36" TSL. Anything bigger and you really should go on and put one tons under there. My Scout 44's didn't last one trail ride when I went from a 35 Bogger to a 38 TSL-SX. I broke one rear axle, and one front axle and bent the rear housing even with a truss on it.
Now I run 39.5 x 18" Boggers with the little lugs cut out. They are sitting on a Dana 60 front, 14 bolt rear with 2.5" springs on top of the axle, traction bars, hydraulic steering and the fenders cut to the max. I don't have any issues with steering, rubbing or breaking.
You can get the tires under there with the lift combo and new wheels you mentioned above, but you are going to have serious problems when you get off the pavement.
Think about what you really want to accomplish and waht I said about the one tons. Anything less than that with a 38" tire is going to require frequent band-aids.