From you description I guess that you're not using the hardware serial interface but that crippled SoftwareSerial. Don't use SoftwareSerial if you need any other hardware part that relies on interrupts to work.
Getting the wiegand protocol and the ModBus library to work on one UNO is not a big deal if you use the hardware and not a badly coded software emulation.
Please post a wiring diagram of your setup and the code you're using. I'm quite sure the problems you have with the Mega2560 are hardware (wiriing) related and not a software problem.