Formatting hard drive containing old OS

"Depending on how you answer these questions, there are several possible solutions:
Solution 1

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Solution 1 is the minimal solution. The operating system is simple to reinstall without data being affected, such as with an update.
Solution 2

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Solution 2 simplifies data backup. Archive data is no longer changed and does not have to be backed up continuously.
Solution 3

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Solution 3 also simplifies data backup. The operating system and data can be backed up separately in image files.
Solution 4

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Solution 4 is a good solution if you want to store Web sites, tools, and so on, temporarily. Then you can periodically format the download partition." Reinstalling Windows XP Home (Part 3): Creating partitions

Since somehow 7 ended up on the wrong type of partition to begin with you can see how it should have looked by comparing the two images 1)booted in 64bit RC host 2)booted in 32bit RC with boot files, mbr still on host. An image taken from a bad install to begin with would only restore a problematic situation onto a new primary.

Like I suggested before especially with a new SSD being looked at the second drive can simply be reformatted and used for storage as is or see the present partition replaced by a fresh primary allowing for a clean install of 7.

If this had been a primary then the manual construct of a new BCD store would be an option for seeing the drive made bootable where you could then try a repair install. The best option now of course would be backing things up from the drive and seeing the corrections needed.

The 2.0 of that still isn't out of beta yet! The section on recovering the Vista boot loader identical to 7's is seen at Recovering the Vista Bootloader with EasyBCD - NeoSmart Technologies Wiki

I still think you are trying to save a sinking ship to start with. Wanting to lose Vista entirely you could easily boot up with a live GParted cd, wipe the partitions on both drives completely, and start over fresh with 7 on the former Vista drive. That would also provide you with the second cleaned up for use as an internal storage device there.

The two things I'm looking at are 1)any problems as a result of the installation on the wrong partition type as well as 2)hardware profiling in Windows would only see the same things repeat themselves once any image was restored from the extended to a new primary.

If it had a nice working install on a normal primary backed there wouldn't be any concern when going to rebuild the BCD store and boot information in general. By this time knowing all important files were already backed I would have had 7 up and running with all programs installed fresh.

7 installs "much faster" then previous versions making that process easier to see done. Plus that insures the best overall results. I've done that enough times here already just to get familiar with both 7s under various circumstances.

(then maybe I'll attach a 32bit RC vhd and restore the Vista HP SP2 Reflect image back onto the original Vista drive at some point.)