1) X and Y axis losing steps- I spent a bunch of time tweaking the pots on the stepper drives, and couldn't totally eliminate the problem. I'd get 1/2 way through a print, and it would lose some steps and ruin the print. Eventually I tried reducing the x/y "jerk" setting in the Marlin firmware, as suggested by some people on the mendelmax google group. That seemed to work pretty well.
2) tangling of the filament jamming up the system - I printed out a cool filament spool holder right after I was able to get the printer running. For the most part it worked ok, but I was getting random tangles where a few wraps of filament would come off the spool and get tangled with something, jam up the X axis, and cause a lot of missed steps, thus ruining the print. Right now I've stopped using the overhead spool mount (currently shown in the photos in earlier blog postings) and I have the spool off to the side of the printer on a dowel. I think I'm going to rig up something with a guide tube to keep the filament under control so I can go back to using the overhead spool mount.
3) filament feed problems into the extruder- I've learned that your extruder MUST keep the filament properly aligned with the hobbed bolt, otherwise the filament will slowly drift off to the side and stop feeding properly. I ended up putting a couple guide pins into the extruder idler piece to do this. I also was able to order some M3 x 50mm SHCS so I could use springs to keep an even compression on the idler, rather than just cranking down the screws.
4) 1st layer adhesion- I'm using "abs juice"- ABS dissolved in acetone - painted onto the glass build plate. That works pretty well to keep the first layer stuck down during the print. This, in conjunction with a 100 or 110 degree C build plate works OK. I'm still getting a little lift / warping at the ends of large parts. I've also used blue painter's tape with the hot bed. This seems to work OK for small parts (1" or 2" on a side max), but parts any larger tend to warp and pop off before the print completes.
5) z-lift- enable the z-lift between moves on your slicer- I'm using a 1mm lift- this helps reduce breaking the part off the build platform during prints.