Regarding charging the client. I usually give an estimate prior to the work. If I see the estimate won't be enough I usually tell them that something isn't as expected and that I'll need manufacturer's support. If they are ok with this we keep going.
In my experience, it's never a problem with the hardware itself, but you never know. I spent 3 weeks last summer debugging a problem with the MRF24WG0MA, and was almost convinced the chip was defective, until I realized that Harmony configured a few things incorrectly (the interrupt polarity being one of them). But yeah, for a show stopper issue that I'm not making any progress with, I would just get in contact with the manufacturer.
No, I've never even worked with a microchip at all before. I do front-end web development normally. I am actively combing through the ADC section repeatedly, yes, to no avail so far.
Feel free to email me if you want a second pair of eyes. sean at [myusername].com
If it's possible, it is indeed possible.