This kind of upgrade works fine if changes are only to an "extra" css file and header/footer and pix.
Changing the standard css files in the distribution when customising is dangerous because these are the ones that will (presumably) be altered by developers.
I have found this to my cost. Now my plan is to maintain just one css file which loads, and therefore overwrites, all the others with the elements I want changed. Unfortunatly, things still break but that is why we love coding for different browsers isn't it
hope this makes sense!