Royal Purple oil has no Molly, there are a lot of things that make a great oil and Molly is one of them in my opinion. There are much better full synthetic oils on the market, Redline, Amsoil, Shaffer, Penzoil Ultra Performance all are top of the line with good Molly numbers. The Royal Purple oil filter is hands down the best, part number 20-820. If you ask the people at the parts store they will tell you a different number and the oil filer is really small. Made for later models with electric power steering.
The platinum NGK plugs are for newer model trucks with different coil packs, don't use them. Run the copper 30k plugs.
The Catch can is always a good investment, never to late. I went with Billet Technologies. Very easy 15 minutes to install.
No need for a new throttle body, I would pull it off a clean it when you add your CAI. S&B is well made but it's all personnel preference.
PVC, definitely pop in a new one.
Flush all the fluids, definitely. Changing the tranny fluid is messy but not to bad, I went and got a kiddy pool from Wal-Mart and let the fluid drain out, the pool kept the fluid from draining all over. It's worth it trust me.
Deeper gears is hands down one of my favorites, you in a 4x4 or 2x4?