Such changes I have done in the past. Pitfalls are:
1. Forget to remove an extra mounting post and the board didn't boot.
2. Had to change the power supply to meet the new power demands. Light reading at http://www.tomshardware.com/howto/20040122/
3. Had to reinstall the OS. Since I backup some 3 different ways, this is always a nice idea since I get a clean machine.
I currently run a Microstar 6534 ver:1.0 which I'm told is not a fantasic board by any stretch of the imagination, I must say I have to agree after trying to flash upgrade and then swapping my Award BIOS chip unsuccessfully. Then trying to swap my 64 Mb NVidia MX2/400 graphics card for a 256Mb NVidia FX5900 Ultra also unsuccessfully - error message "Parameter is incorrect" showing every time an attempt to load drivers/ software.
So, as I think the problem may be down the the AGP speed/voltage, I am going to change my mobo to an Intel D865 GLCLK.
My question is: Can I just take my old board out and replace it with the new one in a straight one for one swap using all of my existing hardware? (I know I will have to change the SDRAM to DDR)