when makerbot were taken over, things went rapidly downhill.
They have yet to improve.

which makerbots do you have neil ?
There is no reason you can't drop a standard board in and just use as a replicator clone - kinda ironic, but at the end of the day a 3d printer is just a collection of stepper motors and sensors (just endstops for the replicators).
Most boards work with most printers.
As do most firmwares.
As the rep 2 only uses one motor per axis - then pretty much any board that supports 2 extruders will be able to run it.

The problems started with the version 3 (I think) that's the one that had no heated bed, and did they roll out the so called 'smart' extruders - which turned out to be anything but :-) - for them as well ?
Those 2 things pretty much killed makerbot as a serious company.

Replicator 2's should still be decent bits of kit and easy to fix.