When my Blitz 99 was doing that, it was actually a hard drive problem. The drives Midway used normally (Quantum Fireballs) are REALLY touchy about their power rails and will spin up/down constantly every time there's a little blip. I fixed that (before rewiring my JAMMA harness with more larger power wires - previously each pair in the power section had only 1 18ga wire) by powering the HDD separately, which was easy since I use a PC PSU in the first place. That stopped the constant spin retries and also fixed my graphics. The game appears to not wait very long for graphics to load and seems to just fail in a mode of displaying untextured blocks if it can't load things up in time.
Also check your IDE cable. It seems very picky about length. The cable that came with my setup wasn't quite long enough to properly mount the HDD (NOS kit ---my bottom---), so I substituted from my box o' computer cables, but I had to finally find a short one (or you can make one) to get it working reliably. In this case, though, the symptom was that it wouldn't cut over to the HDD loader (where it identifies the game as Blitz 99 and then gives the title screen) from the ROM loader (where it does the self-tests).
If your self-test function is disabled (it's one of the DIP switches in group 2), re-enable that. I have a manual for original Blitz if you don't have a manual. It may find something wrong. There should also be a drive check in test mode that you may want to run.
In other words, check your HDD again and make sure it's not still spinning up/down and that your image is good. If all else fails, I can dump the ROMs (I already imaged the HDD) from my setup and you can try that since mine does work. If there's a separate security device, I'd have no trouble sending you those images (especially since MAME can't actually emulate Seattle in realtime).
The hard drive seems to be working fine. The self-test was enabled, but once it ran, it just reset itself and would run again.
At first, the hard drive came up bad, but like I said, I threw a new hard drive in and the test ran fine.
I have a regular blitz manual too, and I couldn't find any help in there. If anyone has a blitz 99 manual, that may be of some help, but I don't really know.
I would like to try replacement roms, but I don't have a way of replacing the roms, other than buying new ones, but I haven't found a source for those either.
I also have a completely working blitz board. Could I just swap the three roms and try that? The reason I ask is because I don't know, and can't find, the information on what the upgrade consisted of. Was it just the roms?
Also, my old board was 2 player and the new one is 4 player, but from what I understand, that is managed by the roms. Do you have information on how to wire the board for 4 player? There is a separate board on the control panel for the 4 player one, but I haven't no idea how to wire the thing.
Lot of questions with this stupid upgrade, but I knew it wouldn't be easy.