so for anybody else who is wondering or searching for a non-booting issue with ANY of the IT games boards with the eagle bootrom after replacing the drive... get yourself a 27C080 ROM... (the original eagle boot ROM was a one write only chip) and write the v2.09 code to it. this will fix the boot issue with the replacement drive. this is why you often see replacement drives being sold on e-bay with a new bootrom included.
http://forum.arcadecontrols.com/index.php/topic,129311.msg1384459.html#msg1384459the lowbrow technical explanation for the issue is this:
the original drives manufactured by WD had a setting on the drive controller to be compatible with older "dumb" controllers...basically the drive came configurable as "single" drive or "master with slave present". we don't actually do that anymore because the controllers are smarter now and can sense there is another drive on the cable. (thank god for SATA) and allows any other drives connected to pipe up for themselves.
In the olden days, the harddrive, when initialized, waits for a "ready to connect or what??" signal from the system.
so "single" would respond "i'm good to go, let's do this" and then it would boot up
a "master with slave present" would respond with "i'm good to go, let's do this, and also i have a friend that needs to be acknowledged too, here he is" and would shutup and let the other drive send it's "i'm good to go, let's do this".
The problem is, because this is a very stupid and old system, the system relies on the first drive that responds to also say "oh yeah, i have a friend here that needs to be asked if he's ready to go as well." but because this type of handshaking doesn't happen with new drives, the eagle bootrom sits and waits...and waits...and waits for a drive that doesn't exist to respond. Which is stupid because there is no instance where 2 harddrives would ever be connected in this system.
the new version of eagle bootrom sits and waits...and then times out and goes on booting with what it's got.
what throwing a CD rom drive in the mix does, is changes to another boot code section in the rom in preperation to update the software. initializes up the CD rom drive, then queries for the harddrives (ignoring any that dont come online asumingly because they are defective and we will deal with them later in the update screen). the system attempts to boot off the CD (which it does not find) then defaults to the detected drive in order to boot. Which it does.
it's a stupid setup.