Its fixed. The problem was that x was not 90 degrees from y. Stupid me should have thought of that. I was thinking that the gantry was square didnt even think thats the x axis could be a skew. I was able to slot the bolt holes on the gantry and adjust with a tsquare and is pretty accurate for right now. My plan is to make taller gantry arms later and the problem will be completely fixed.
thanks for all your help