This may not be of any help but i'll try.
In many cases cloning the drives work just fine. But, in the past i have ran into issues similar to you where the cloned drive just wouldnt boot.
With Acronis, what I have found to work the best is just creating a Full image of the entire disc. (Not just partitions)
You'll have 2 option going this route.
1. A straight up Full disc image. it will restore the entire disc to any other HD without issue. If the new disc is larger you'll end up with some unallocated space at the end. You can still extend this space to the main partiton once in Windows.
2. Sector-by-Sector full Image. This option will allow you to resize each partiton before restoring the image. Quite useful if the target disc is smaller than the Master Image, or if its larger and you can assign the additional unallocated before hand.
Sector by Sector will also be larger images. For the most part, its really not needed to do this unless you just prefer to.
The downside to this is youll need a secondary HD, partition, or other place to at least store the master image.
However, If it is a fairly clean Image, (not lots of Music,Pictures etc) you can burn the Image to a DVD or DL DVD.
Then, you simply boot from the Acronis Rescue disc, and when it asks for a image location, swap the rescue disc for DVD or DL DVD you have with the target image.
Now, the target system doesnt need to have a secondary HD.
I have never had any issue doing it this way. With cloning I have had a couple problems.
As far as your question about a repair disc, I would say Yes,
If for example you choose to restore a image of just the main partiton, excluding the 100MB boot one, Windows will fail to boot. But a System Reapir will fix and get you going again.
My guess is that the same would hold true here.
You mean, will the repair disc wortk on any computer?
I believe it has to match the system type (32 or 64bit) but other than that should work on any system.