Home built machine setup, perpendicularity

I am looking to put together my own home built CNC machine with
linear rails and ball screws onto a heavy tube frame. I am trying to
figure out how to drive the main X axis which will move a gantry
over the table. I am contemplating using 2 ball screws(smaller ones)
to drive each set of trucks. This way I can assure no racking
problems and have increased machine stiffness. My main questions is
if I go to the 2 screw system and I am using stepper motors how do I
initially when build this machine get my X and Y axis perpendicular?
Assuming that each X and Y rail setup is straight to start with.

Basically can I measure perpendicularity on a 3' x 3' linear rail
setup with something like indicators. I do not have access to any
large right angle plates or things like that. I would think that
there would be some clever way to measure this.

I used to design machine tools for several years so I know all the
basics but when we did this setup part it was all done with a laser.

Thanks
Scott