Gateway just sent me a new motherboard, I know how to install it and everything, is there anything besides the BIOS/CMOS I have to set again, like autoexec.bat or config.sys or dossstart.bat, BOOTLOG,TXT?....Everything is the same in the PC, just putting in a new motherboard, do I have to change anything?.........and on a new pc if I build one, what will I have to create when I put in the motherboard?

the motherboard doesn't have anything to do with software (those files). if gateway just sent you a replacement, then it should be all set to go as far as upgrading goes, either before you remove the old one, or boot into safe mode with the new one, just remove all of the "system devices" from device manager, and any other drivers that are no longer needed (if the old mobo had onboard sound, delete those drivers)

If the boards are identical it might not be necessary to remove the 'system devices' but it's probably a good idea to do it anyway.

You shouldn't have to delete any of the drivers. When windows boots up the first time on the new MB it will recognize any new hardware and ask for the windows cd. It might take 2 or 3 reboots before windows recognizes and installs everything. Besides if you delete drivers you can't be sure you won't delete newer drivers not contained on the windows cd such as upgrades, modem and sound card drivers or drivers for other add-on hardware.