I'll respond to your list in order:
1- Lanes skill shot is the least valuable anyways. The slingshot (not a pop bumper) up there is meant to be pretty weak, so that it can go back up the lanes a couple times. However, it is intentionally turned off in software after a couple hits, so it doesn't stay up there forever. For skill shot, you should go for a short plunge to your upper right flipper to try for one of the other 3 skill shots (Witch, Haunted, or crystal BALL)
2 -Should hit the pops. Check the wall up there and give it a slight tweak outward so that the ball will hit the pop instead of blow past it.
3-Autolaunch should feed orbit most of the time, but I wouldn't get too hung up if it doesn't
4 - If you're seeing rescue letters, I would be willing to bet that your Castle Door switches need adjusting. If you're seeing Toto or TNPLH, you likely have a flaky switch in one of those areas. Go into switch test, and pound on the playfield a bit to see if anything is too sensitive.
5 - It's not intended to be clear. You get a audio trigger each time a switch down there is hit. So if your pop bumper is going crazy and hitting a bunch of switches, you get a bunch of audio calls going off.
6 - They're not intended to be easy. But certainly doable. The TNPLH pop can kick the ball back out onto the playfield either up through the outlane, or power slam it off the center post (tip - always hold up your left flipper if the ball is in TNPLH, so you create a clear path if it does happen to catch the center post on a power-shot off that pop bumper). TOTO turns off the pops, because that mode is all about the 1 or two shots, and creating randomness from the pops insn't conducive to that. With TNPLH, the trees can help feed your rainbow letters quite nicely, so they're enabled on purpose.
7 - Throne room should hit your left flipper
8 - There are a bunch of extra balls in the game. Read the rules in the manual and it will help you find them all. Couple off the top of my head: Yellow Brick Road 10 times, and then again at 50 times. Horse of a Different Color completed correctly with 5 horses, 10 Fireball Frenzy Jackpots, and some more...
9 - Calling is best
10 - As long as you don't insta-cycle the game (on off within a second), you're fine. Absolutely no issues with turning the game off, turning it back on a minute later, then turning it off again.
11 - What LLoyd said. Set it lower for lock 1, and fiddle with it from there.

Congrats on your new game. We put a lot of time and effort into making it. Still putting in tweaks to code.

PS - I put up 3 million in my game at home on Sunday, with a Toddler handicap (my one-year old likes to stand on a chair infront of the game and slap around on the glass and lockdown bar and hang on my arms). It was my best game ever played.

Cheers,

Eric (EE for WoZ, Hobbit, DI, and something different for POTC)