Bicycle Tutor

I recently got back into biking (I havent since I was in high school, when I used to spend countless hours on the bike). I was looking for a bike to buy mostly for all around mountain trials and found, no surprise here, that they run way more than I can afford. I then found a used Specialized Endure Comp from 2004. Buying the bike I knew it had a dead front suspension and that most likely a lot of other parts will have to be replaced but I read a lot of great reviews about the bike so decided to go for it.
   

The bike looks and feels like it has never been taken care of or serviced. Today I cleaned the rear cassete from piles of old grease and dirt. I did a run with it in the mountains of Jerusalem, and the bike did really well both downhill and uphill. The breaks weren't as tight as I would want them to be and the gears didn't shift smoothly but those are minor adjustments. Or so I thought. I tried to adjust the rear derailleur and found it to be acting weird. On the 9th gear it was bent so low that the lower part of the chain was rubbing against the upper. After cleaning the cassete I put the wheel back in place locked it and alas it does not spin... I tried to push the brake pads back, messed around with a nob on the brake mechanism and now the break doesn't work. The handle is completely loose.
It seems like the problem with the brakes isn't a new thing because there are round scratch marks on the discs. The break disc sits uneavenly and touches the right side of the breaking mechanism.
   


At this point I would love advice on how to proceed from here. I'm at the beginning of my bike adventure and in pretty deep. I did hours of reading on different parts and setups and so far bought a used RockShox Reba Dual Air. I'm looking for an affordable beginner solution that will allow me to ride and enjoy the trails.

Things I already ordered:
Mineral Oil to bleed the breaks
Fox seal kit for the rear suspension

Parts I considered to put on the bike:

Sram x7 rear derailleur (not sure what the difference between long and short is)
If the breaks need to be replaced: Shimano DEORE BR-M595 + new discs


Here is the picture of the disc break on the back wheel. How do you remove it if it has no screws? The rim is Mavic XM 819.
   


Thank you for looking and any help!

Man way to high tec for me and too much work. Once you sort it out it should be a good bike. But I am old school and like simple bikes that can be worked on easily. Hard to tell what your problems are. If you squeezed the brakes with the wheel off you pushed the pads to far out . You can try pushing them back or you will need to dissemble the calipers and rebuild, that fill and bleed the system. That is a complex bike to work on. Good luck.......

Your brake disk are Shimano center lock; Google is your friend.

Make sure you use Shimano's recommended fluid in the brakes - other wise you'll be purchasing complete replacements - including tubing.

Are you sure your new fork will fit?

Cassette - just replace it, and the chain.

With your wheels off, re-do the bearings, replace the balls, regrease - I like boat trailer wheel bearing grease for all my bike applications - cheap, water resistant, lasts for years in bicycle applications.

You may need a new crankset, and BB.

Your probably need to replace your headset bearings.