As has already been said, you want to deal with the texture and orange peel issues sooner rather than later because, over time, the paint becomes harder and cures.
How many coats of clear did you use?
3- 4 coats would give you a good margin if beginning with 800 or 1,000 grit, anything less... be sure you are absolutely comfortable going with 800- 1,000 by hand. A pneumatic D/A palm sander will be your friend for the large flat areas but you'll ,obviously need blocks for the transitions and such.
You don't have to refine to 3,000 and instead could stop @ 2,000 or even 1,500 but again, it's how comfortable you are with the sanding process and the buffing. If you hate machine polishing, then finish with the finest grit you like.
What paint system did you use?
I am not going to comment on 3M polishes because everyone has there favorites and what works best for them... however, M105 & M205 are certainly as good as any 3M product. So, I would not necessarily go out looking for new polishes BUT if you want to spend the money- so be it. I would consider M100 as well, if you are absolutely going to look for new products. M100 is purely solvent based (M105 is water base with solvents) and has a longer work time (less dusting) and a larger load of abrasives in the set.
Forget foam for removing 3000 marks... Will foam do it? Sure. But wool and rotary @ will do it faster, with less heat created and remove or minimize any 1,500 marks that were left after refining. Glide coat may also help you when refining in the sanding process. You can work M105 @ 1,000- 1,200 rpm and it will cut just fine.
For pads... Lake Country/ Buff & Shine make great 7- 8" pads for the rotary and as long as you clean them between sections with a brush or spur and after use wash and spin them out... they will last just as long as any other manufacturer's pad and you won't be paying 3M's incredible prices.
And I would give it 90 days for that paint to off gas before applying a wax/ sealant. If it hasn't been baked or IR cured... then it's going to take a little longer before you can apply a protectanct. Actually, M305 from Meguiar's (introduced last year) is a body shop safe, durable glaze that will provide some transitional protection until you can put on a wax/ sealant.