Z-squash, dimensional accuracy, and other help needed!!

Hey folks,

I'm relatively new to the 3D printing community. I have an Anet A8 (Working on upgrading to an AM8), I upgraded to Marlin, working on installing 2 mosfetts, waiting on BL touch and e3D hot end. I am running on a mirror for my hot-bed and it seems to work really well. I got rid of the old H frame for the y axis and added belt tensioners.

Okay, so enough with general specs. So, my issues are these;
Z print seems squashed on my prints. I also get some small gaps in the prints which makes me think it might be missing steps. I am using Hatchbox PLA, running around 200deg for the nozzle and 60 for the bed. I have calibrated the Z , e-steps by mechanically measuring 100mm of movement and adjusting e-steps till I hit 100mm repeatedly. I did the same for x and y which now give me very clean holes (circular) but the dimensions are still slightly off, about .2mm depending on the print..

Next, I'd really love some advice on step-by-step calibrations steps to optimize my printer. I see loads on e-steps and heat-towers, but haven't really seen on anything that's remotely definitive when it comes to, check this, then this, etc..

I wanting to print some gears that I designed, (Small) but I'm really wanting to be able to predict the measurements and have them actually work.. I'm at a loss for things to check at this point.. so many options.. so little information.. :P Thanks for any advice / help!!