Sorry I can't help you with any of the trails in Santa Fe - I live in Albuquerque but.....................
for altitude sickness: drink water drink water drink water
I usually make sure my dad starts drinking water 2-3 days before he comes out here for a visit, and I make sure he carries water with him at all times. Don't stop drinking once you're here and plan on taking it easy at least your first day here, Albuquerque downtown is at 5000 and you'll just go up from there no matter where you go!
As for the ferry up and ride down: you'll have to check with the bike shops but there is a ski resort in Santa Fe with a paved road that leads up to it, that may be what they're talking about vs MTB'ng, but again check. Dress warm if you do that, Santa Fe itself is 7,000 but the top of the Sangra De Cristos is *shaking head* I don't know 11,000?.....12,000 so it's gonna be colder up there!
and Last: if you're going to be here in Sept it can still be hot although monsoon should be over by then so the humidity will be low again (thank the stars!) Just be aware it's very easy to dehydrate in this climate without even knowing it so Over drink, your body will get rid of whatever it doesn't need. and bring lots of sunscreen, the sun is more intense at these altitudes!
Hope you enjoy our beautiful state!
Life should NOT be a journey to the grave with the intention of arriving safely in an attractive and well preserved body, but rather to skid in sideways, champagne in one hand, strawberries in the other, body thoroughly used up, totally worn out and screaming: "Yeah Baby! What a Ride!"