I have a Fender Fat Strat.

When I got everything on and all the screws in I put a string on to see if it was back to normal but the string was hitting pickups. How can I fix this? Do I basically just have to take everything off and try and lower the pickups? I got new pickup covers and they seem to be partially the problem, but the strings are also hitting my humbucker too. Also, it looks like the strings aren't aligned over the magnets right, did I just reverse them on accident or something?

Can anyone just give me a detailed answer on how to fix my problems, this is really pissing me off.
JUst losen the screws next to the pickups
"Blues is easy to play, but hard to feel."- Jimi Hendrix
That seriously all I need to do? and then is the alignment for the strings and magnets a huge deal or anything?
Don't worry about the strings lining up with the magnet Poles.

You need to tighten up your pups before you put gaurd on. You do the reverse of how you took it apart basically. Once on, you can lower to taste.

Is your pick gaurd screwed down flush now? Did you get a new pick gaurd? Is everything else OK?
I took apart in like January because I got a custom paintjob done on my pickguard, but right now I'm just trying to loosen the screws. My hand is hurt and tired from putting them in too tight, haha. I can't get a few in tighter to make it more flush, but aside from the pickups being too high everything is fine.
well in that case I would check over in Guitar Building and Customizing Thread because it sounds like your new paint job now has holes with paint in them.

You could take a small drill bit and drill it out a bit. ...pun

Maybe start with a tooth pick and see if you can clean all those screw holes out first.

Is that the problem or do you have other issues too?
turn the screws at each end of the pick ups the other way, you would loosen (counter clockwise) them to lower the pick ups.
Nah, it has nothing to do with the paint, it's just got to do with getting the pick ups at the right height, which is weird because before I took it apart they weren't loose but to make it right they're loose now. And I just got a rubber handle screw driver and we're back in business now.
Okay, so I got everything figured out basically, except I don't remember the screws ever being weird, do I just need to take the pickguard completely off, align the screws within the pickups, then once that's set put the pickguard back on?
Seriously at this point I'm considering just taking it to a guitar store and getting this done, it's just really annoying.