Did 'nt you post about flying into Mexico City then going by bus to Huatulco? With an inflatable this should not be too much of a problem.Not sure how compact or heavy a min i-me is.I have lugged a duffel with ducky -two break down paddles -Pfd-helmet -pump -booties -paddle pants and rash guard -waterbottle with built in filter -throw bag -minimalist wrap kit (slings, biners, pulley), plus day pack for clothes, toileteries, reading materials, and camera.That is a enough stuff to lug around on buses.
Adding a kayak and skirt complicates things.The buses,especially the one you want for a long trip like that, are very nice and professionally run with a large cargo hold underneath.A creek boat might not fit.They might charge extra for do many bags /kayaks.One duffle for boat and another for gear between two guys would probably work.For kayaking a two.piece apx. 210 cm paddle barely fit in the biggest duffelbag REI sold.How long are your raft paddles?( longer than 105 cm I assume) .The taxis in Mexico City are 95 % Volkswagon bugs.There are several bus terminals for different companies and for different directions.Research ahead of time to avoid chaos with a bunch of gear and no. clue.If you are lucky, the station within walking distsnce has the bus you want.If staying in Mexico City for a while ( recommended) there should be lockers ore storage of some sort at the airport.I 'd rent a car if taking kayaks.