What now - very much depends on what you NEED to achieve.
Although 64 bit installation may also be used to install 32 bit, the license ONLY covers either the 64 bit installation or the 32 bit installation NOT BOTH - in usual circumstances.
In otherwords, as I understand the situation if you purchase Windows7 64 bit you may decide to install 32 bit., as your system is not ready for 64 bit. When it is you can then on the same motherboard (as Microsoft see a new M/B as a separate installation) or by telephone call to Microsoft and if they agree, you can uninstall the 32 bit and install the 64 bit.
What I do not think you can do is install and run both 64 and 32 bit from the ONE license.
I appreciate that ALL the above may be entirely irrelevant to your circumstances as YOU may have TWO licensed activated Windows 7 O/S
Depending on how the dual installation was set up, if your objective is NOW to boot and use the 64 bit installation and I read correctly that you cannot do that then you will have to rebuild the BCD so that the 64 bit installation may load, without the other HDD that has the 32bit installed.
Your first approach is WITH the HDD of the 32 bit NOT installed either F8 and if there is an entry REPAIR your computer and then the normal options under Windows7 including startup repair try that first.
If not boot from the Win7 DVD and follow the same.
If that does not work you will have to select cmd prompt and then follow the link for the BCD (Boot configuration Data rebuild)
Do not forget that the drive letter may well be changed in the Windows RE. again see the link.
NOW to the question of the MFT - as you probably know that is where the system looks to find the contents of the drive including the Boot files etc., as each single file on the drive is referenced in the MFT, which is on the first block of the drive.
TRY running the chkdsk with the drive in an external enclosure or docking station.
IF the MFT is damaged, then you are either looking at verifying the state of the drive with the manufacturers disk check utility - always best if you are not unfortunate enought to have a HDD of which gthe manufactruer does not provide one, in which case use Seatools or WD check that will run in limited generic mode on any drive.http://www.tacktech....ay.cfm?ttid=287
you can try this but I have NO DIRECT knowlege of its use, I have read reports of it being quite successful. and if it is IT should I think be seen ONLY as a temporary measure while you ascertain the state of the drive and replace if necessary.http://www.cgsecurit...g/wiki/TestDisk