Have you tried Startup Repair from WinRE (Windows Recovery Environment)?
Hookup the two SATA disks the way you want them setup and follow these steps:
0. Boot into Vista installation DVD
1. Choose your language settings and click Next
2. Click Repair your computer
3. Choose your operating system and click Next.
4. This should bring up System Recovery Options.
5. Click on Startup Repair
Startup Repair should now start diagnosing your system to identify the root cause (we know that anyway) of the failure. Once it has identified the root cause, it would automatically start repairing your computer. If you are curious to know what Startup Repair did, you can click on the details link and see which tests Startup Repair ran to diagnose the problem.
After Startup Repair has finished the repairs, click Finish to reboot your computer.
Your computer should boot normally into Vista.
Goodluck!