So I noticed an unusual thing on one of my cuts. The tool follows one path in the y direction and then when you return, it follows a different path.
Any things i should be checking first?
Check to make sure you are starting square to your table, most use the hard stops as a reference.
You check this by drawing a very large rectangle and checking the diagonal differences of the corners. as large are your cutting area. If they are not under a mm in difference, chances are you will travel two paths.
Another thing to do is program your very first move to air cut the bounding box of your job. That moves the machine past all the extremes and verifies it returns to the exact same starting point, and verifies this will not travel two paths.
Another option is you are hitting something, catching the hose/wires, or just trying to move way too fast.
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Thanks forbthe feedback! I think it was a bit from every point…in the end i cut new rails with V grooves so i know the y gantry isbtracking square. I then tweaked my end stops as well…i think every time it homed, the one backed up a bit.
It all seems pretty square now!
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That is exactly what I did!
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How deep is that groove? 
About 1/2" (13mm). works great and I would highly recommend it be included in standard lowrider2 build instructions…
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Thanks!
Was it difficult to make sure that the two tracks was parallell to each other? How did u achieve that?
Not at all–i just set up the fence on the router table and ran it through…although if you don’t have a router table and have to do it by hand, I would suggest some kind of guide. As far as mounting goes, I laid it on on my box beams and just made sure they were equidistant from each other and referenced the same points on the beams (since the beams were square, it was fairly straightforward)
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I got a router table. Best thing ever! 
Thanks for the advice! I will try this out and report back!