So, the V4 patch was applied correctly (sorry to have asked the question, but there's SOOO many people that doesn't read instructions).
The first thing I would try is to check IDE configuration in Win 2k. Sometimes, flashing a firmware can cause problems with IDE devices (DMA not enabled anymore, devices not detected,...). You can try to remove both IDE channel, then reboot. After the reboot, win 2k will re-detect these devices. When it's done, you can try to put your drive in the PC.
Can you also try to patch your drive to v4, in your other computer ? So when you put back the drive, you already have the good version, thus avoiding unnecessary upgrades.