Vista x86 to x64 Upgrade Boot on x64 Problem

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Hi, I've just upgraded my Vista x86 system to Vista x64. I ran with x86 on one disk and did a complete fresh install on another disk. On boot up both Vista options come up in the boot menu but if I remove the x86 disk then I get a boot error, no boot partitions found. I can only think that on install of the x64 Vista it already saw a master boot record on the x86 and did not install it on the 2nd disk. Therefore, as I want to wipe the x86 disk and just run from the x64 do I have to install the MBR and will this mean backing up the disk first to do it and then a reinstall from backup? Or can I make it the primary MBR without risk of loosing the data?
 
Thanks for the info Conan257, been having a good read about this all afternoon. From what I can see though nobody is doing what I'm trying to do in that the MBR is on the x86 and I need to get the MBR on the x64. Is it a straight forward as disconnecting the other drives I have and just leave the x64 connected. Boot up with the original Vista x64 DVD and go into repair. From there in the DOS prompt type bootrec.exe /fixboot and this should reinstall the master boot record and now make the x64 the master boot disc? Or do I have to use EasyBCd to backup the MBR from the x86 and restore it to the x64 partition on the other disc?
 
OK, went into Vista repair and command prompt. Typed bootrec.exe /fixmbr and it came back command completed successfully. Ran bootrec.exe /fixboot and it couldn't see the records there, probably because the command is for a previous boot loader such as XP. restarted Vista and still didn't boot. So reconnected the original drive with the MBR and then started into Vista x64. In disc manager now it reads that the d: drive which is my x64 partition now has "Heathly (boot, page file, crash dump, primary partition) but unlike the other drive that has the MBR it doesn't say Active, System. So if I now do a right click on the drive and select Make Partition Active, will this now make this the main boot drive and make it the System Active drive and can I deactivate the other drive so this controls the boot loader?
 
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