I have used both drivers and didn’t notice a difference. You shouldn’t need active cooling on your drivers if you are driving them too hard they will over heat and have a thermal shutdown and will miss steps instead of blowing. If your axis aren’t moving easily loosen all the bolts. Get it moving real nice and slowly tighten it up. Mine is very loose, the rigidity comes from the geometry of the design not how tight you have the bolts.
If you make it a little smaller your miss-alignments should go away. Triple check all distances X and Y and diagonal. just make sure the corner blocks are the same distance apart in the x and Y directions. Once those as good measure Diagonal across the middle those should be the same as well. Do that before reprinting parts.
Sorry to hear about your bad experience with the MK9. The 3 I am using are the most trouble free extruders I have ever used including an E3d I use at work. Did you see my walk through on some of the common MK9 issues? http://www.vicious1.com/import-extruder/ Most come pretty good out of the box, some need a tune up.
Sorry you are disappointed at the performance of your machine. I’ll do my best to get you up and running if you still have the desire to get it going.