I would like help with CTC 3d printer upgrades

Hello all. I would like to start off by thanking everyone for any help. So I have bought a CTC 3d printer(Replicator 1 clone) with the dual extruders and have done many recommended upgrades. I am currently running Sailfish 7.7. I have bought an Azteeg X3 Pro mainboard and a VIKI 2 LCD to install. I own Simplify3D and Netfabb. My questions are concerning the firmware. I have a Prusa I3 that I run Marlin on RAMPS board. Does anyone have a good working Marlin sketch for the Azteeg and VIKI 2 for the dual extruder setup? Or another non proprietary firmware? Also I was looking at the Mightyboard  and it looks like some of the endstops are hooked to the MAX plugs. When I switch to the X3 Pro do I need to duplicate those hookups? Because the X3 does not have any headers for the MAX endstops. So I would have to source those headers. I also need help with the pinouts to put in Marlin for the cooling fan for printing and what needs to be set for VIKI2 sd card and USB functionality. I Used USB with my Prusa I3 and print directly from my PC with S3D and have never experienced any problems so would like to do the same with this printer. Again Thank you for any info and help.