You can leave a bike at the Aduana in Zona 1, Guatemala City. They will give you a bit of paper that says your bike is being held by them.
BUT. And it´s a big but, you can only leave your bike with them while Permisio is still valid. You get a 30 day permisio when you enter the country. It can not be extended without leaving the country.
Fine for overstaying a permisio is 30 Qetzales a day. approx 3.75 US$.
You can leave through any land border and return through a different border on the same day. If you want to return through the same border, you have to wait 3 days.
I couldn´t get the bike out of the country cause of an accident, so had to pay the taxes and get the plates. There is a plus side, though. I don´t have to pay for any border crossings in Central America.