Rhothgar,
Sorry you're having the troubles.
1. It's essential that BIOS is the latest version. Clear CMOS, then download the new BIOS on the working system to a flash drive and install on the problem system. Try running Windows again.
2. Take the HD from this system and try in the working system- not in SATA0 but the next open connection-SATA2 or whichever. If Windows Explorere can see the files, the problem is in the software, possibly a corrupted boot partition.
Wild speculation: I'm wondering if the boot partition is still set to the orignal Vista size, but Win Ultimate uses a much larger one- (1GB now I think). The installation worked at first but then the boot partition became filled to overflowing.
If the working system can't read the files, based on the Boot Manager missing error, it may be that the HD has bad sectors. Take the HD from the working system system and try in the problem system. If the copy of Windows is OEM, it may well just work and that wouold help isolate the problem.
3. The second session might be to try a repair install on the problem system drive. Insert the disk or drive used to install and select repair. That however, can take as long as a clean installation.
4. Try reformatting the problem drive. Install a free version of EaseUs Partition Master in the working system. Install the problem disk in the working system and run a test on the disk for bad sectors Reformat the problem disk twice. [BTW, in Partition Magic, you select the task and then "Apply"]
Run a test on the disk for bad sectors. Use Partition Master to clone the working drive to the problem drive and activate using the key provided. If the systems are using an OEM OS, they may activate automatically.
4. Format the problem disk in place using a command prompt and reinstall Windows using the product key.
Let us know what happens!
Cheers,
BambiBoomZ
z420 > Xeon E5- 1660 v2 / 32GB / Quadro K4200 / Samsung SM951 (256GB) + Intel 730 (480GB) + WD Black 1TB
z420> Xeon E5-1920 / 24GB / Quadro 4000 / Samsung 840 250GB + WD RE 1TB
z620 > 2 X E5-2690 / 40GB / Quadro K2200 / HP Z Turbo Drive (256GB) + Seagate Constellation ES.3 1TB