I actually clicked on this for the transport question but then answered your followup....
I use Montezuma Expeditions for shuttle service when I need to, they go to all the towns you mention. On the rates page they have a PDF of the times the shuttles actually travel, so you can match it up with your flights to figure out what might me best to start /end the trip. (Although in the off season it's mostly mornings, I think).
You can make arrangements in advance, Montezuma Expeditions usually speaks really good English (just go slow!). They'll want you to fax or e-mail confirmation information (most companies will) with charge card info (most will in my experience).
Although if I was leaving Montezuma and heading to the airport area I'd take the Directo bus from Montezuma; it's twice a day (6am-ish and 2pm-ish) around $14 a person and it's always been air conditioned when I've taken it, except for the first leg from Montezuma to Cobano (10 miles) for me it's always been a bus I have to switch in Cobano.