How to reinstall OS without losing installed applications

Hi folks,
Question for you about software installations and if they can be backed up to overcome the need to reinstall them when reinstalling the MacBook's OS.
I have a newish (bought last Autumn) 15" 2.3 GHz Intel Core i7 MacBook Pro running OSX 10.9.5 which I spent a terrible time installing my beloved (but dead) 13" MacBook Pro's "brain" to.  I did everything wrong and have actually got two OSXes (the original preinstalled Mavericks and the copied-over Snow Leopard)  Of course since I had been running my equally beloved and neolithic Snow Leopard on it there were issues with the versions of expensive software which suddenly couldn't run/be installed.
And after another heart-stopping round of purchases, this time of the minimum versions to run on my new MacBook Pro which included Final Cut Pro 7 (I had used FCPro 6 till then) and Photoshop CS3 (I was off the charts with my version- but it was mine, I paid for it!) and second-hand (since new was no longer available in the versions I could afford) I ran into the awkward problem of not being able to install Photoshop CS3 because although I had the original disk and the real serial number from the vendor, they'd not deregistered it.
Fortunately I was able to get a bypass from customer support at Adobe (because everything was kosher- just so ancient) BUT it means that I have to keep this installations of it or lose it (and probably have to prove myself all over again.  It took days and many hours on chat and the phone to get them to tell me what proof they needed and what could be done and how that I cannot go through this again and keep my sanity).
And now to my present day issue-  the MacBook Pro is not stable and there is a weird pop-up asking me to complete the installation for "Application" and I am concerned that it is somehow a bug.  There are freezes and crashes I have never encountered before and today I even had to force shutdown of the Finder, something I have never ever had to do with any of my previous 13 Macs.  Photoshop's Bridge causes crashes, Final Cut Pro 7, though massively improved speed-wise, can be "skittish".  iTunes behaves weird and my iPhone being plugged in can do very odd things whenever an otherwise OK cable is used.  Hard drives sometimes refuse to be ejected for no reason whatsoever.
What I would like to do is to start over with a fresh install but to ALSO save my current installation of Final Cut Pro and Photoshop, the two bits of software which I need to have and which I worry about losing installable copies of.
Bottom line:  can this be done, ie can I selectively back up not just data but ALSO software installations?
If not-  is there a way to make the MacBook Pro "happy" once more without doing a complete reinstall?  It was reasonably OK with having renamed the imported/copied version to User1 and having placed itself into hiatus so it might not be that?

Clayton,
Spend the £20 it will cost you to get a new internal DVD drive, preferably one that the Mac OS supports and that you can burn CD / DVD on.
The pain and suffering this will save you over the lifetime of the G4 tower is worth it, believe me.

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