MakerBot Industries

MK6 will solve your all of your problems! Seriously, no reason to run a DC motor. The tuning is easier, it's 100 percent consistent from one day to the next. You set the profile once and done-that easy. Bite the bullet and get the upgrade kit since you have a MK5. ALso, get one of the new black nozzles as they make a huge difference too. They don't have the tip dragging and catchign the plastic making fill and layers much smoother. Totally worth the cost!! I've upgraded 3 cupcakes so far and the owners cannot believe the difference.

Shameless Plug: I maintain the master list of Cupcake upgrades at http://www.thingiverse.com/thing:8636

And yes, moving to a stepstruder of some sort (MK6 or one of the printable self sourced variants) is the single biggest quality upgrade you can do. Since you have a MK5, I would suggest http://www.thingiverse.com/thing:5795 to do a stepper upgrade on the cheap or a MK6 kit to do it on the easy.

After that, doing something about the Z wobble will help with your bigger prints.

Try cleaning your build platform with a bit of acetone or rubbing alcohol when is is cold and off, that always fixes my adhesion problems.

Align BP? or Level BP?

Adhesion - live on the wild side - A little 500 grit sandpaper and try a wipe with 'Goof Off'. Not Goo Gone. Then an occasional wipe and you're good.

Assuming you mean level the build platform, try this: http://www.thingiverse.com/thing:6558 using three springs as I describe in my copy.