You'll have no problems at all, I did the same thing twice back in'06. When you import the bike they will give you 6 months, if they don't just ask for it. The difference in the passport stamps is just that your "Entrada" stamp will have a tiny car symbol on it indicating you drove in, and your "Salida" stamp will have a tiny airplane symbol on it. People do this all the time and have no issues, just be sure to bring the bikes import paper/sticker back to Mexico with you when you return so you'll be able to properly clear the bike out when crossing into Guatemala.
Enjoy the ride, I've previously done Central America, and am currently in Peru, I can tell you border crossings down here in S.A. are much more organized than in C.A.