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Yeah, they're helpful on the phone but if you're there in peak season you're gonna need to book well in advance or have a very large window so you can take other train options. Even we didn't get our first train choice on the way back in first week Oct, even though we only saw 2 other pairs doing the ATM trail - I guess there's lots of MTBers doing day trips that we don't see.
Did you pre-book your bikes on the various trains? That was the problem we had getting back from Inverness to Edinburgh - no bikes without reservations, and no reservations available.