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This is in reference to an R1 purchased in 4/2013

So I am one of those people who hasn't been able to use the whole entire build plate. I now think the issue is a tower being a bit more than 90 degrees from the build plate. First question is it possible for this to be my issue. I can get the center and the three points in front of the towers to be correct but I get lifting between the towers, and quite pronounced on one of them. My thinking is that if the tower is leaning away from the build plate the further away from the tower it is the "shorter" the arm would act causing the print head to be too high. Is this conjecture correct?

Assuming that I am correct is there a software adjustment to correct this? I am guessing there is not but if anyone knows of one could you explain how to do it?

I know the correct solution is to get the towers perfectly perpendicular but that is not an easy solution at this point. When I built it I leaned the towers in as far as they could go so I probably need a new top plate to truly fix this issue (if I recall there was a bad batch or two around this time in regards to the top plate). A new top plate means a massive rebuild and I just don't have the stomach for that at this point (I have put well over 100 hours building, rebuilding, calibrating, upgrading this machine that I have less than 70 hours of build time on). Outside of the build plate issue the printer is performing well.

After further thought I had something wrong in my previous analysis. If the tower is leaning away the further away the effector is from the tower the lower the arm plate is therefore the further the tower pushes the arm making the arm appear longer and that pushes the nozzle higher (if the arm was shorter it would be pushed down I think).

So looking at the tower with the biggest issue I saw that there was a little bit of room for adjustment. I loosened it up and pulled it in as best I could. It was only a partial correction but got me close enough so that I could try some hacks. What I ended up doing is putting a shim opposite of my troublesome Z tower to correct for the tilt.
There is a lot going on in the photo to explain. First even when cold my rev2 heating plate is much higher in the center than the edges so I have shims underneath everywhere I put the binder clips so I don't flex the glass (without them the edges are .8 mm lower than the center before heating, makes calibration tough). On the bottom is an adjustable shim that I used to correct for the tower lean. The print is what I use to do fine calibration, there is a piece at the center, in front of every tower and across from every tower. This is the first time I got all seven locations to be usable.

While this isn't an ideal arrangement at this point I am not looking for style points. I am cautiously optimistic this will work but have much more testing to do.