And just for reference :
Software versions:
40600 Complete GTC
40500 GT 2005
40501 GT 2005 Extra courses
40400 GT 2004
40401 GT 2004 Extra courses
40300 GT 2003
40200 GT 2002
40100 GT 2001
Unfortunately if someone pulled the U53 or swapped it at some point there is no way to "know" just by Looking at it, what the board version is. Unless you pull the U61 and read it that is. Or put chips on it and power it up and see what it says.
So your original board was a 40600 and the board you bought on Ebay was a 2004 40400 Every version of Fore from 2001 through 2006 had the same boards, with a few changes. some were tournament, these had extra processor and some other chips installed, then the "normal" older green boards. They then switched to the RED boards with ATX power connections (because they were having some issues with power draw on the Green boards causing the JAMMA fingers to burn.) This is also the reason for the add-on power harness that connects to one of the 4 pin molex plugs on those boards. That was there "fix" for the power issues.
Green and RED also have 2 "TYPES" 8 RAM chips and 4. 8 being the most common The 4 chip version was used on some Big Buck Hunter games. As far as I know nothing else used that setup.