I have bought a 2X4 router and have completely rebuilt the machine it was very cheaply made. I was cutting ovals and it looked like I chewed them out (polycarbonate). Now I can cut a perfect (by eye) circle and it has a very smooth finish. One more problem to overcome, I hope. 
I am cutting polycarbonate. I am cutting two pieces that are to be assembled to gather. This is where the problem lies. The two pieces do not line up; the gears that go inside don't fit. I took the g-code and cut the pieces out on my CNC milling machine and they are perfect. So I am assuming this eliminates the g-code.  Info on the router; Mach 3 – steppers - rack and pinion - Bosch palm router.   Can anyone point me in the right direction of where to look.

Can you post a pic of the parts, might gives us a clue as to whats wrong.
Hood

I am on my way to the shop I will post them when I get there thanks

You will have to try again with posting the pictures of the parts. Nothing saved.

Tweakie.

one more try

heres them side by side you can also see a finished product on cut2spec.com

I just checked my steps per uint with a dial indicater it seems to be moving the same amount each time

mach 3 verison R 3.00 is what I am using on the router I compared the part from the milling machine and the part from the router there is almost .250 difference in length

Not really sure what I should be seeing in the pics as I dont know how they differ from what they are meant to be.
 Just wondering if you have any offsets for the tools in the router, that could possibly account for it.
Hood

How do I check the offsets?   I will try to explain the pics. The two parts are riveted together, when I do this the out side edge of each part do not match. I get something different everytime I cut it. It is the same drawing for each side. The parts lined up perfect on my other machine. It is like the steppers are losing a step or mach 3 is giving the wrong signal. I think I have eliminated this possibility buy checking the steps per unit with a dial indicator. So I am at a loss. Could the mach 3 be set up wrong The computer and mach 3 came with the router.