Moving system to another HD

I've got Win 7 U 64 installed on a 2-disk system, both disks identical 300 GB, one partition per disk, both partitions active, Win 7 being on disk 1, the boot manager ended up on disk 2.

I'd like to transfer this Windows system to a single harddisk (newer, faster, 1TB). So I partitioned the new disk with 200 MB (for the boot manager), 300 GB and 600 GB (approximations).

Then I tried to get Windows to the 300 GB partition, by making a System Disk backup and trying to restore it to the new disk (my plan was to then use the Repair Disk to get the boot manager and settings adjusted to the new situation). I also tried to install Windows from scratch on that new disk and then do a restore from the backup taken of the old disk. Windows got put into the 300 GB partition, the Boot Manager into the 200 MB partition, just as I had hoped.

I'd like to use Win7's features to get the files copied in the new Win7 disk layout at sector 2048ff, not the old disk layout, that's why I'l trying to use Windows own tools exclusively.

Anyway, Windows didn't want to restore the backup to that partition, the Repair Disk kept telling me it couldn't do it, either because there was no backup for this Windows installation, or because the boot manager was missing (although it was there, in the 200 MB partition), or also without an explanation.

So I was thinking about copying things to the new disk using Clonezilla, but I can't find any info telling me whether it follows the new Win7 disk layout or not.

Does anyone know how I could do the trick using Windows own tools? And if not, has anyone tried something similar using the usual clone tools (Acronis, Ghost, Clonezilla etc.) and knows whether (or how) that would work?

And does anyone know a clone tool that will use the new disk layout?

Thanks in advance for all replies