Transmission: The low-hanging fruit move would be to drop the transmission pan, install a new filter, and add new fluid. The better move would be to proactively replace the torque converter with a billet-backed TQ to head off the common problem with the factory JMBX converters warping, which causes hot-spots, and leads to clutch/friction material wearing off, which circulates through the tiny passages of the transmission. This can lead to issues. Additionally, the factory transmission tuning isn't optimized, which can also cause longevity issues.
Engine: The AFM/DoD system is a known issue, and many folks opt to either have it physically removed with an AFM delete kit, or simply have it turned off with an ECU tune.
You can optimize the engine and transmission tunes with an aftermarket solutions (ex. BlackBear Performance) which costs more, but gives you the best case results without tearing in the engine/transmission. (best)
A popular & cheaper option is to buy one of those Range OBD dongles that tricks the ECU into staying in V8 mode full-time. (meh)
There is a tuning service where you send in your physical ECU, and they will permanently disable the AFM programming. (better)
You can also disable the AFM system by shifting into Manual Gear 5 (diagnostic mode), which is perfect for around town driving, but you'll notice the lack of 6th gear on the highway...
You can do the tune & replace hardware (AFM delete, new torque converter, etc...) and really extend the life of everything, but you pay more.
Like most projects, budget dictates decisions.
