I also plan to have 2" more clearance to the X-axis carriage, but my plan is to do it in two areas.
I raised my y-rails in the pan 3/4". To do this, I added some additional side and bottom gussets to the vertical Y-rail tubes, made new taller and wider side plates that bolt to the Y-rail vertical tubes, made brackets that clamp the Y-rail vertical tubes to the legs and then filled the opening below the Y-rail bar with concrete.
I plan to have a 1 1/4" Y-X spacer, but currently just have 3/16" ones which will get me to 6.5" X carriage clearance.
Pictures of all this work are in my build thread: Build Thread w/ Mods - fieroguru - #76 by amosdudley