Marc,
Congrats on getting your Kitfox and saving it for a new life of flying.
Can't say that I have ever seen wrinkles like that; and, speculating how it got that way is anybody's guess. If it is not due to physical damage, maybe incorrectly installed fabric or something that developed with an incompatible paint/solvent system - who knows.
When you strip the fabric you will be able to determine if the structure is ok - if so, as it seems to be from your examination, the cause of the wrinkles may just have to go as one of the unsolved mysteries of all time.
Having the time to refurbish and install new fabric and paint is certainly the way to go.
Sincerely,