New Mac Boot Drive -- Bunk Application Migration

Hi. After upgrading my Mac Pro 1.1. boot drive, I used Migration Asst. to install the clone I had created. Unfort. many apps weren't not working (OS X 7.5) after that.
So ... I did it again. The apps were now all working, but they were being launched from a app entitled folder nested withint the system apps folder (the one with the app mark). 
When I tried to replace the non-working app folder with new, it said couldn't.  Can I?  I don't program, but can successfully follow code/commands to imput into terminal.
Please advise!
Thanks in advance!!

Lion lacks Rosetta, no support for PowerPC, but confused over your placement of root level /Applications

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