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Kym- you can apply for an FM3 after you get here. I suggest going to websearch and look for secretaria de relaciones exterior web page, when you get on it click on english version and look for requirements for fm3.
when you cross the border they will give you 6 months. which means you have to have the car back across the border before the permit expires are pay a fine... I personally got tired of doing that, its better to use public transportation, there`s plenty and its cheap. if you get an fm3 it`s better to buy a mexican vehicle.
Queretero is a nice town, fairly large, they have opal mines there. lots of industry. Cant tell you much about roads to Manzanillo, its out of my region, I`m in the Puebla/Tlaxcala area.   good luck.  Bob

Thanks Bob, Since I wrote this request i have changed my route. I am now headed through the Yucatan area along the caribbean and then on to the pacific side. I have all the time in the world so i decided why not. Thanks for your help. Kym

Kym,
Don't know if you have left yet but your route sounds very 'odd'to get to Manzanillo from Calgary. Obvious route is cross at Nogales. Pacific coast route to Manzanillo via Puerto Vallarta. Three days - comfortable drive (if you use the toll roads).