Having the ballscrew on the back on my machine has crippled the stiffness of my Y-axis and although the distance is greater, that shows how the effect can be significant.
Correct Jonathan yours was a huge distance from centre hence your issue. Switching would save a lot of hassle having to sort extras like seals and way covers etc. My suggestion was a sound one but the choice is yours of course. BF your design is a good one i would like to point out and will work great without the changes so well done. Building these things is a costly venture and you spent the time listening and looking at what works already. Mine is no way near as good as what you have so you should be in a good place.