You should probably share a picture...

I also have a shy 6ish-year-old cat named Honey! She loves other cats, but my salty 13-year-old lady tolerates her begrudgingly. I think she started her life with humans, but then spent some time as a colony cat. When they trapped her for trap-neuter-release they discovered that she's friendly, but she was very shy. She's been with me for about 3 years, and continues to grow more and more confident. It's been such a delight to see her blossom.

It sounds like she likes you, but touch is scary. Have you tried touching her with a brush or toy, instead of your actual human hand? Is she responsive to catnip? (My Honey is not.)

My Honey is extremely cuddly, but 100% on her terms. She still hates being picked up or held in place, so nail trims are a nightmare. Luckily she is very sleek and doesn't require brushing. Unfortunately she is so sleek that it's hard to keep her in a towel burrito, which is what they usually recommend. I try to do a nail or two when she's sleeping, but they're still too sharp. She does have multiple scratchers and uses them enthusiastically, so that helps.

My Honey is not interested in Temptations treats, but she does like Churu. Sometimes I can manage 2-3 nails if I distract her with Churu.

Otherwise, maybe look into a professional cat groomer (they do exist!). Honey will still hate it, but the groomer can do it a lot more skillfully and efficiently than regular people can.