I, too, agree with ScottW’s suggestion: my Lulzbot Mini 1.0.3 had the same problem (wiping too far back), and replacing the 1.0.3 Y motor mount with the 1.0.4 part fixed the problem!
Interestingly, simply replacing the part didn’t, at first, solve the problem. The 1.0.4 Y motor mount has two pair of Nyloc nuts and screws, that screw against the ends of the Y axis rods. When I first installed the 1.0.4 part, I noticed the belt was suddenly loose, so I (against the assembly instructions) tightened those two rod screws until the belt was tight again. Then I printed a test print, and was terribly disappointed to find the nozzle still wiped too far back on the wiper area. So just replacing the part didn’t solve the problem.
Then I re-read the 1.0.4 assembly instructions, and noticed that it very clearly said to tighten those two Y rod screws only enough so that the tops of their heads were flush with the face of the Y motor mount. So I unscrewed the screws to that point, which made the belt very loose, then I tightened the belt, and Voila! The printer now wipes right in the middle of the wiping area!
Here is what I think is going on: the nozzle wiping is now effectively a dimensional error test - which is actually useful. If your Y axis is too long or too short, the nozzle will wipe too far behind or ahead of the wiping area. I imagine this is because, as ScottW pointed out, the 1.0.4 firmware changed the Y axis reference from the back endstop (whose position changed with the 1.0.4 parts) to the Y axis front endstop (whose position was common across all Mini models). If your 1.0.3 Mini had a too-long Y axis, the 1.0.3 would have no problem hitting the wiper area because it’s so close to the back endstop. The same too-long axis on a mini running 1.0.4+ firmware will miss the wiper area, because it’s so far from the front endstop that a Y scale error across that distance accumulates a few millimeters of error.
When I inappropriately tightened the new 1.0.4 Y motor mount rod screws until the belt was as tight as it had been, I was adding a few millimeters to the effective length of the Y axis, which caused Y dimensional errors, which in turn caused the nozzle to miss the wiping area.
When I then loosened the 1.0.4 Y motor mount rod screws to the distance described in the assembly instructions, I was reducing the Y axis length, which required me to tighten the Y belt. …and now my printer works great, hitting the wiping area every time.
So, whatever the reason, replacing the 1.0.3 Y motor mount part with a 1.0.4 version, and installing that part according to the 1.0.4 instructions, fixed the problem for me - thanks, ScottW!