our cat Jango was a stray as well, and exhibits a lot of the same kind of behaviour. a lot of it is just learning to read their body language and responding properly, which you will learn over time. Jango hardly likes to be petted at all, he will tolerate quick scratches and a couple pets, but he gets irritated quickly and nips (he nips NOW, but when we first got him, he bit. hard.) and he also doesn't like to get picked up, he used to scratch and bite to be let down. all his adverse reactions have cooled over time as he's learned to trust us, but he (and you cat too) may never get to the level of cuddly that a lot of people expect for cats.
for instance, spending quality time cuddling with jango usually involves lifting him up so he can sit in my lap while I do things on the computer, watch television, or pee
. he doesn't like to be pet or held, but he does like to sit on laps. or he'll sit beside me on the couch, or lay beside me on the bed, with maybe his back touching me if I'm very lucky.
for the feet, I might wait a few days so she can learn to trust you more, give her lots of treats and be very nice to her, but don't push too much with the petting unless she comes up, and once she's more used to you touching and restraining her, I'd start playing with her pads just a little. a little massage, and making very nice voices at the same time, but back off if she gets mad. (I always say sorry when I annoy jango, I feel like he understands it from the tone of my voice.) jango used to HATE when I would try to touch a foot, and now he regularly falls asleep on my lap while I massage his feet. cutting his nails the first few times was hard (it helps if you can get someone else to hold him, while you deal with the foot) but now it's super easy and I can do it alone.. but mostly what you need is time. also, maybe try a play session with a laser or something before you play guitar and then she might be tired enough to not attack.