Problems with Gift Certificates/Coupons since upgrade

Hi, I would really appreciate some advice please. I just wanted to warn you that I am not technical. My store https://www.bunnyzoescrafts.com was created in June 2008. Everything has always worked fine until September 2010 when my technical support upgraded my store. Since the upgrade my gift certificates or coupons no longer work. They mis-calculate and also I have noticed when testing that I can place an order using a funds from a gift certificate but the balance would remain unchanged so the customer could then order again with the same funds.

My original technical support was unable to resolve this issue so now I am seeking new help. I have contacted a company in the UK and this is what they have told me:

*Bad news I'm afraid - there are approximately 180 files which do not appear to have been correctly upgraded.

The problem facing me is that although I can work out what 3rd party modules have been added, I have no idea what, if any, other customisation has been done. I can also see the history of the upgrades and that on 6 Jun 2009 it was upgraded from 1.3.7 to 1.3.8 , on 23 Sep it was upgraded from 1.38 to 1.3.9f and then to 1.3.9g on 29 Sep...but I can't say which of those 120 files should have been upgraded at any particular stage. There are some files which were created in 2005!

The only way I can see to fix this is to start with a fresh installation of 1.3.9h and then transfer across your changes and re-install all your extra modules. This will require probably around 10-12 hours in total (£450-£540+vat) - so you may wish to take this up with your Technical Support lady who I assume charged you for her efforts? If you do, I recommend you get her to give you a detailed breakdown of the procedure she intends to follow, but she should NOT carry out the work on the live site

If you do engage us to do this, then I am going to need full Control Panel access in order to set up an additional database and (hopefully) to be able to work with compressed files to save time on upload/download.*.

Surely if I do not have problems with anything else in my store a re-install is unnecessary? Is it not just a problem with the files associated to Gift Certificates and Coupons?

I would really appreciate any advice you can give.

Kind Regards,
Nikki x