When you boot the computer after changing CMOS battery, setting Windows Time will also set that in the BIOS.
However, if there were system settings that was changed from default, any of these are wiped out. Chances are if there are any that needs resetting, you'll know, or will soon. This is why otherwise computers has jumpers, to not perform a full reset of the computer, just what has to be.
I'll go on a limb & say that if you were running a much newer computer since, one thing that cannot be fixed with a CMOS battery change, is the speed of which the PC operates. There'll be times when you'll feel frustrated, though considering it's from 2004 & boots, and otherwise was running well before storing (the 5 years not used somewhat preserves the hardware, if wrapped or boxed properly), you're doing good.
You may wish to move to a newer OS for your security, however I'll leave that decision up to you.