1. Body mount chop ( kit available on line) $45+/-. A welder will charge you about $150 for the work.
2. Upper Control Arms. I went with Fabtech.
3. Three (3) inch suspension lift w/ adjustable coil overs with resivoir up front and taller springs and resivoir shocks in the rear. I went with dirt logics.
4. One (1) inch diff drop (not required but will allow your CV axle joints to articulate better with out constant stress on the joint.
5. One you go up in tire size your RPMs will be off and your truck will search for gears all the time. If you live in a hilly area you will need to think about gear set upgrade to at least 4.56. If your going to pull a 2k + pound trailer this is a must. May even consider 4.88s if trailer heavier. The gear change is matched to your tire size and RPMs desired (power / fuel economy). Seek out an expert to do the work! I went with Yukon 4.56s. I pull a 3500 pound Geo Pro trailer. I should have upgraded to 4.88s.
6. Stage 1 front fender chop. See YouTube. It's a do it yourself job. Easy. Take your time. This will give you a much better approach angle and will eliminate all tire rubs in the front.
7. Remove front mud flaps and cut plastic inner where you find it rubbing. Usually done in tandem with body mount chop. See YouTube.
8. Tire size. With the above mods you can easily run 295-70-R17 with no rubs. I'm running 285s.
Why did I upgrade my TRD suspension. The simple answer is that I destroyed it and a brand new set of stock tire size BFG KM3s doing a bucket list trip to Deadhorse, Alaska this past summer. The roads were trecherous and the pot holes came in herds! Since I had to change it anyway, I went bigger / better.
Stay away from wheel spacers. Waste of time and money. Dangerous. Will stop the rubbing on your UCAs, but will rub finder well when under flex in a different area.
Since your suspension is brand new you might be able to do a leveling kit. Can't guaranteed it won't rub.
No rubbing under ANY conditions with my set up. I just ran Imogene pass. Performed perfectly.
I'm also running a full Gobi rack and full cbi armor. No rear seats. Built custom cargo boxes to fill the area (3 sheets of plywood). My empty weight with two (2) adults and two (2) dogs is 5540lbs.