MendelMax printing help (weird prints)

I've got a mendelmax 1.5+ that I've built and have been using for about 6 months. I'm in the process of printing the parts to build a second one but recently started having issues printing. The top, bottom, and front come out great. The back and the back to edges (back left and back right edge) have been coming out really really terrible. I've tried to physically trouble shoot and have come up short. I have not changed anything in my marlin firmware in months, I've been pretty much using the same slic3r config for months too. Of course I'll change the infill based on the object. I've included some pictures of a 20mm hollow box. The pictures included do not have the top on it but I have two of these object printed and the top prints fine, I just didn't want to waste any more filament.

Since noting has changed I'd check:

1) Cleaning the rods
2) Lubrication
3) Loose bolts
4) Y table hitting the under structure of the frame
5) Y end stop wire (or other wires) catching the table.

I have checked all of the items above. I've popped off the belts and can slide the X and Y axis without any resistance. I have a buda 2.0 nozzle and replaced the tip with a brand new one to see if that might be the issue, but no change. For testing purposes I am able to extrude 100mm @ 400mm /m and it's very fast and smooth, I know this isn't really a useful test but it's something I tried.

The box on the left was printed at 100% flow and the box on the right was printed at 90% flow. The top and bottom on the 90% flow does not fully create a flat surface but looks like planks due to the gap.

Right now I'm printing at:
Dia: 3mm
Extrusion Mult: .9
Layer height: 1mm (never given me a problem before)
Infil: .4
Infil every: 2 layers
Temp: 230
Speeds are all the Slic3r 9.10b defaults

As you are printing, what's going on?

My guess would be that you get blobs of plastic on the print head and the motion you have set up in Slic3r pushes them to the back of the print. I know that watching a print for an hour isn't all that exciting... The reason could be moisture in your filament. You might try puting it in a warm oven (< 150C for ABS, lower for PLA) for a few hours to dry it out.

What size nozzle are you using?

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Waitaki 3D Printer

.35

A layer height of 1 mm with a 0.35 mm head means that you are pushing a *lot* of plastic on each layer.