heating and engine running very rough

I just purchased a 1999 chevy malibu. from the time we got it home i have had a overheating problem. we replaced thermostat and seemed to not overheat now. however it now runs very rough like not on all cylynders. i was wandering besides sparkplugs what else could it be. also i need specs for timing. i was also wandering about the fans. they apparently are not coming on. we replaced fuses i was wandering when they sopose to come on. also wipers stay on till car is shut off. and the trunk release does not work. any answers or help be greatly apreciated