There are two revisions of the Viper board. One with the IDE port populated and a newer BIOS, and one standard with IDE headers removed. Aside from that, everything is identical. The only known games that have the IDE port populated are ParaParaParadise and Mocap Golf. It is confirmed that you can use a Mocap Golf PCB to replace a bad ParaParaParadise PCB as long as you swap the security chip. It is probable that the same repair works in the other direction.

All other games are theorized to be compatible with each other as long as the security chip is transplanted. There is no currently known way to populate the headers to use a standard game with PPP or Mocap Golf.

The security chip sits just below the RTC-RAM chip and appears at first glance to be a standard 3-leg transistor. Examining the part number reveals it to be a 1-wire EEPROM chip containing the security of the system. It can be transplanted to another board without harm given careful soldering technique.

The hard drive in a ParaParaParadise Viper will eventually go bad. If you dump the drive using DD or a similar command, it will be a 12 GB file. However, only about the first 512MB is used. It is safe to use a 1 GB CF card as a replacement if you image only the first 1 GB of the dumped drive onto the card. To use the card in place of a hard drive, you will need a CF to IDE adapter. The Viper will recognize the CF card in the adapter as a standard drive and boot fine.

I've had issues with some newer CF cards not booting in the Viper stack. My suspicion is that they are too fast. Try to get a CF card that is 133x or slower. Transcend 16 GB 133x CF cards have been tested working on multiple setups and multiple CF->IDE adapters and are available on amazon.