The error messages indicate some mismatch between system files or app files.
For instance, an app is seperated into the apk file, runtime libraries, odex files and dalvik cache. If one of these files does not match the others -> trouble.
Also, there are depencendies of apks on the underlying Android framework and within the Android framework files, there are also dependencies.
So, to me it looks like some file got replaced and now does not meet file dependencies.
But all of this is related to data and system partition only! No need to hassle with other partitions...
The problem with some restore sets is, that they do not flash a clean data partition. This may lead to problems, so to be save, I recommend a full factory reset after applying a restore set, such that data and reader partition get formated and on next boot get re-initialized.
But you can - indeed - copy the partitions one by one and as long as you do not touch the raw boot area (first 24MB), it should be relatively save...
In your case I would do the following:
1.) Make a new backup of the partitions of your faulty reader.
2.) Make a backup of the partitions of the good reader.
3.) Do a binary comparison of the backup images! This way you'll know for sure if one of the partitions other than data/system/reader is corrupted... And finally you will only have to restore the bad partitions.
Here is a descriptive list of all partitions: