How do you fill the holes?
You've got a lot of questions, the search option is going to be a good friend of yours. There's more info on this site than you could ever hope to read.
I think the best way to fill the holes you're asking about is with that expanding, hardening body foam, then sand flat and paint over with a strip of herculiner. User "MountaineerGreen" has done this perfectly (along with others). iI you run a search, you'll find a step-by-step.
Does anyone know a good way to get brighter, nicer looking headlights?
Brighter headlights - yours don't look fogged or anything, so I'm assuming you just want better bulbs. You can go with Sylvania Silverstar bulbs - which a lot of people have on the site - to give you a brighter, whiter light. If you're really looking for superbright, you may want to invest in an HID kit. Otherwise, there are diamond clear headlight housings you can buy on eBay that make a big difference.
Also, I accidentally broke the cigarette lighter, pushed it to far in. I dont even smoke!!! But it looks stupid. Is that an easy fix? The metal casing is just inside the dash!
The cig lighter should be an easy fix, you can pull the trim around the radio out and take a look to see what's wrong with it. Not hard to pop it back into place or order a replacement and solder it up.
How much is a lift kit? I read that was pretty stressful on older vehicles... I do want it to last a good long time. Is that true?
Lift kit will run ya about $200-300. I don't think it's a big deal on older vehicles. Plenty of guys have done it on their Explorers, myself included, and had no issues. I lifted mine when it was 9 years old and have had no issues in the 3-4 years since.