Not sure about getting replacement the control boxes, but I want to ask you a question.  Have you had any derailment problems with these #6 switches?
I am thinking of buying a few, but I have heard both praise and complaints about them.  One indivudual claimed he can't run a train over them w/o a freight car derailing....

This question right to the Bachmann I suppose.   I would like to purchase various E-Z track items in HO and N but would like to know if I can buy the track and roadbed unglued?   I was able to take the track off the roadbed of a piece of 18" radius NS in HO.   I enhanced the roadbed to make it look as if it was on real stone ballast.   The reason I ask is as an active duty military person I move around a lot and during moves, the ballast on your layout will be lost. (I found out in 2004 going from NJ to Germany)

i.e. Can I buy (aka special order from the factory) a bulk box of 36" HO straights without the track glued to the roadbed?   I am on to something that maybe Bachmann would like to see as it blows the competition out of the water.  

The E-Z track gates will work after some enhancing as far as gettting the gates to stay down with little or no bounce.  Try adding some couter weights in the middle of the gate or drill under table, glue a piece of thread to the bottom of the long plastic piece that the train runs over.  Than clip on a small fishing lead split shot.  This will work but it will take patience in the placing of the counter weight.