You have to pull the cylinder to replace the base gasket so just start there. See what shape the cylinder is in. It might be ok.
I rode my DRZ, after splitting a radiator and loosing all the coolant, until the cylinder discolored. I was certain that I caused damage. I got the radiator braised, put new oil in it, and have been riding it since. I hear noises but it must be all in my head because that was about 6 years ago.