Yea you shouldn't have any problem installing Roms on mjb just make sure that the ROM you install does not install a downgraded bootloader or you will brick the device......also if a ROM uses the ne4 bootloader you will be stuck using the ne4 modem
No rom should ever include anything but the system and kernel imo. Ive personally never run into one that includes the firmware/bootloaders, but if you do you should bring it up to the dev.