Migrating Programs to New OS (HD Crash)

I'm apparently having problems with the hard drive on my MacBook Pro. I can no longer start my computer from my main hard drive. I can only start it using a clone I made some time ago.
I talked to a Mac Genius, who told me he suspected a problem with my System folder. He seemed to think it pretty serious. He encouraged me to try and save as much data as possible, but he suggested that cloning my hard drive might finish it off.
He said they'll install a new hard drive for me. He also mentioned something about archiving my existing data/programs, as well as "migrating" software programs to my new hard drive. So I have several questions relating to this situation. Some are a little nebulous, as I don't know all the details.
First, I should point out that I had a recent clone of my hard drive, but I destroyed it when I last tried to update it. I beileve my cloner (I forget if I was using Super Duper or Carbon Copy Cloner) backed up my files but told me the cloned drive wasn't bootable. This was presumably a clue that my hard drive was going bad, though I didn't realize it at the time.
I just tried cloning it again with Carbon Copy Cloner, but it wasn't long before it just quit, warning me that it couldn't make a bootable clone. (I think it said it couldn't locate a file in the System folder, or something like that.) I'm now trying it with Super Duper. When I got home from work, I discovered that it had copied 29.27 GB, but now it seems to be just hanging there, recording no further progress.
So let me ask some actual questions...
1. Archiving Files - The Mac Genius told me he could barely see my internal hard drive. However, I can see it just fine after booting into an older clone - one I made before I installed a lot of software programs. I've copied files from my internal hard drive to another partition on my external hard drive and am now cloning it. (I just discovered that cloning is still in progress; it's just going really slow.)
So when I take my computer in to get my new hard drive installed, is there some way for the Mac techs to somehow archive all the data on my hard drive and copy it to my new hard drive? I'm not too worried about losing data, but I dread having to reinstall and reconfigure all my software.
2. Migrating programs - If the Apple techs are unable or unwilling to archive my programs, would I be able to "migrate" a software program from a clone that isn't bootable? Is it even possible to migrate a software program from files that have been manually copied to another drive?
These are my main software programs:
Adobe Creative Suite
Microsoft Office for Mac
iWork
iLife
MAMP Pro (including my MySQL databases and phpMyAdmin)
I can reinstall most of them easily enough, if I have to, but installing Creative Suite was a pain in the butt. I THINK I might be able to reinstall all the MAMP Pro stuff by simply pasting a folder into my new hard drive. I certainly don't want to have to go to the trouble of recreating my database, all my virtual hosts, etc.
Sorry for the long, rambling post, but I'm just fishing for any tips I can get, and I wanted to offer a lot of details.
Thanks.

your HD is obviously on its last legs and can fail completely at any moment. You should not count an apple techs being able to archive this stuff for you. they can try but it may not work just as it's not working for you. do yourself a favor and back up as much of your own data as you can (by hand if necessary). Migrating applications is only possible from a bootable drive or a TM drive using Migration Assistant. as you don't have either reinstall your software by hand.

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