that is why most of us do our own bodywork/rust repair
the nice thing is you can buy every part for the tf trucks new
for a price 
if you stay with a shop doing all the work then you should probably buy what they need or be prepared to pay the piper
i personally believe that only one company owns the equipment to stamp full panels and sells it under many names/brands
new doors are $600 each plus shipping, plus fitting; figure $800 per door plus painting and any bodywork
fenders are $540, plus, plus; $3 grand just for four pieces would buy a lot of patch panels and tools to diy and you get to keep the tools
depending on the condition of the cowl, vents, cab corners, floors and steps the shop might also suggest a new cab
a new bed, headlight buckets, grill, inner fenders, etc...
if you get out of paint/body jail for less than $20k you will have almost as much in your paint/body as i have in truk minus the motor
i have a couple of friends that do classic restorations, they ask for $10,000 up front to get started with no guarantee of a finish price