I went through this issue a few weeks ago, my machine is a bit bigger than yours and what I did was added elevation bolts at either end of the gantry, but cranking these I can lift either end as well as tilt the gantry forward or back. Then using the rail's I'd installed I leveled them two ways. Next the Z axis is made using THK type rails. I installed gib plates of sorts on each carriage, this allows me to again, tilt the Z axis two ways and gives me fine adjustment for the final alignment. These gib plates will have a small gap between themselves and the Z axis frame which will be filled w/ potting epoxy.
To get your gantry sqr w/ the length of the machine, use a small v-bit in your spindle and mill [ I've a wood spoil board] traverse [along the x ] your mill while cutting a slight groove in the table top, you can then use a large compass to create arc's which center on the groove. Where the arc's intersect is 90Deg to the milled groove. You have to tram your mill to this line. Use a large machinist straight edge and a dial indicator to get it sqr all the way along. Then you can test some parts, measure w/ a caliper and tweak as needed.
If you find a better way, let me know. I' haven't done the sqring thing yet, just the leveling part
Jerry
JerryFlyGuy
The more I know... the more I realize I don't
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)