The new engine has only 11K on it, so I really don't see a need for parts replacement at this time.
I do see keeping a rigorous fluid change schedule to be advantageous for reliability in the coming years: trans fluid, coolant, PTU/RDU fluids, etc.
Yes, the PTU is easier to flush with the engine/transmission out. Only problem is getting the existing fluid warm enough to easily flush. Hopefully not gunked up though, the first time you attempt the flush will tell you if you need to do more than a couple in quick succession or not. I recommend cheaper full synthetic PTU fluid for the flushes, SuperTech should do just fine. For the final fill you can use the full synthetic fluid brand of your choice. My personal favs are Amsoil Severe Gear, Redline Lightweight Shockproof. Many stalwarts are running Royal Purple and Mobil1 also IIRC. Again, key to long life is the change interval more than anything.