Unanswered Z-Axis Alignment issues

I do know that in the brackets do appear even on the brass nut. They are not flush with the bottom of the nut, but about quarter to half inch from the bottom. I'll double check that area and look for something to make sure the nut is tight, right?

 

Alright so I'm still investigating but do you think the Y or horizontal rail might not be straight? When I removed the case I noticed that the slightest touch of that left vertical rail(not the lead screw) caused the right end-stop to trigger. When I applied a little inward force on the rail it homed correctly...

EDIT: I think it's called the smooth rod. I'm wondering if something is wrong with it's support? Should it be 100% straight?

 

I dont know what's wrong with it. I checked everything I could see, not very experienced at what I'm look at though. I leveled everything with a leveling tool. The horizontal rails are level, the vertical smooth rods appear straight and level. The printer will home properly in this position but will not print because the bed isn't level to the nozzle. If I adjust the lead screws to level the nozzle with the bed then the homing won't work because the horizontal smooth rods aren't level now. I can get it to home in that position if I press the left vertical smooth rods inward a little bit. Appears I can't have my cake and eat it too :'(