Did you modify the pullups on Aux3 and Aux4 as required? I seem to remember that at least one of these is tied to a :LED (Status1, I think).
Also, to allow both Home (RA and DEC) and LIMIT (RA) to both work I had to sacrifice the STATUS LED and then modify both the CONFIG.H and the VALIDATE.H file, which had a bug in it. All of this is Onstep 3.16 (speaking from memory) on a MiniPCB2. So the three CGE PROs and the single CGE I did with the MiniPCB2 did not have a Status light, which I find marginally usefully anyway, esp. with an IO pin-starved processor.
I'll dig back into my files to read what I did - it has been over 9 months since I had my hands on the CGE Pros that I modified for friends. I'm a G-11 man myself and operate portable. The CGE Pro is too much to move around.
PS: It can be made to work. However, it is an open question in my mind if HOME is really worth it - adjusting the microswitches to accurately place the axis aligned at the north celestial pole for purposes of initial alignment is very, very, difficult. And the SET PARK/PARK functions are more flexible and useful. But to each their own.