Issues with 12 speed cassettes.  I am having a problem getting it to shift into the last 11 tooth cog on two different wheelsets.  I have backed off the limit screw so much that it has over-shifted on the outboard side so I don't think the limit screw is the problem.  It will actually shift to the 11 and then about 2 seconds later it shifts back up to the 12.  if i hold the button down, it will stay in the 11 but as soon as I release the shift button, it shifts back to the 12.  I did replace the wonky looking narrow/wide type pulley with one from a 6800 ultegra derailleur I had laying around.  That helped shifting all over but the 11 cog is a mystery.  When I use an 11 speed wheel and change it to 11 speed in the settings, it has no issue shifting the entire range.

I bought these IIIPRO Bike Brake Disc rotors, the rotors do not brake as they should, I bedin them for two weeks, cleaned them, pumped the brakes, changed the pads (sram code rsc) and nothing helps, the rotors brake very poorly by their own, after these I installed TRP and Shimano rt66 rotors and they brake well

With tires like these you will limit bike potential to a down-country territory at best. Around 850-900g per tire is kind of minimum reasonable, think of new Purgatory in T7 or T9 or EXO Forekaster as minimum from Maxxis. I used DHF MaxxGrip for all the colder part of the year, considering something little faster for warm period, but never an XC tire.
I would also reconsider simple SPD before you mount them for Shimano trail pedals for better support, it makes difference which is worth extra grams.

Here is the bike.  Sorry for just the one pic.  I have been unable to upload pics lately. 

Awsome paint job! Can you tell a bit more how did you make it? What was your base color?

 The bike was ordered as blue and I taped off sections using fineline and painted with epoxy paint. It looks ok from this distance but no so much close up. I also made a decal with photoshop.