First off, I have to admit, I really don't like the Fancy Breeds TBH.
I like a good old plain smooth or an Abby.
My little boy is good chunky Rex , coarse short fur.
The Peruvian was years ago and I didn't know she was until her fur grew .
(And don't get me started on Satins and Skinnies)
I decided with my Peruvian (Marmite) that she wasn't a show pig (though she was a perfect jet black) so her fur was an apendage on her body, not the be all and end all. I kept her fur floor level at her sides and short round her bum so she wasn't hampered by it ( I saw too many photos of GPs in 'rollers' poor little souls)
Yes she needed combed and bathed but she tolerated it well 
Your guinea obviously doesn't. She might just find the brushing uncomfortable so she's pre-empting it.
Is there a chance you've caught her skin or pulled her fur?
I think, if it was my piggie I'd just trim her fur short, use those round ended baby scissors. She'll feel the benefit in the summer time anyway and the fur will grow back.
Claws, you can't leave, if you don't feel confident then a vet or a local rescue will trim them (Rescues will charge a donation but it'll be less than a vet and they'll be used to all sorts of guinea-pigs, some will be very neglected, scared, stroppy, unhandled. They will give you advice on clipping)
If you don't cut them, the quicks get long, the pigs risk the nails cutting into their skin and in extreme cases they can fracture their feet.
We have two boars, DD and I do the cutting together. She holds the piggie against her stomach, not sitting on their rump, she holds them under the bum and round the tummy (then she'll be in biting range)
I sometimes just do the back feet one day and front the next if they are really tardy. It's not worth winding them up too much.
We try to be quick and efficient (and stern but quiet).
GP3 took umbrage once and .............well I think he peed but I could be wrong 
The chattering is an angry voice but it might be directed at her cagemate rather than you? Ours chatter from time to time, they tell each other off just for walking in between the other pig and the plate