Feral cats can be tough. I applaud you for bringing one into your home. I've had a few experiences myself with one and it can be a challenge. However, I think you've got the right approach. In my opinion the most important key here is patience. Letting her set the pace will go a long way in her trusting you. That being said, there are a few things that you can do.
First, finding out what motivates them can help quite a bit with any kind of training or rehab. Food motivated cats are always the easiest, largely because it's easier to provide an immediate reward. If she is food motivated, giving her a single treat at a time to reinforce positive behaviors (choosing to sit near you rather than further away, any kind of positive physical contact, etc.) can help promote more discovery for her in that area.
We tend to forget that animals are very scent based creatures as we don't have as strong a sense of smell (myself in particular). One of the way cats bond is through scent sharing. They often do this by marking things with the side of their head (where an oil gland is) but giving the cat access to your scents helps promote bonding. You can do this by leaving some of your worn clothing in places or beds they sleep in. If you feel comfortable with it, give them access to your bedroom as well. It's the most scent heavy room in the house and generally cats who want to bond are drawn to it.
Playtime can be a big way to win a cat over as well. Try a wand toy, or one that has a handle with a toy attached to a string. Drag the toy along the ground back and forth around the cat. If you can get them playing then you can expend a lot of that nervous energy and it can really help establish trust. They may even seek you out for playtime.
It's great that they're feeding from your hand, but that may be the wrong time to try petting them. Some ferals can be defensive at feeding time (I know I just said to reinforce with food but, bear with me). Trying to touch them while they're eating may cause their defenses to go up. In my opinion (and it is an opinion) the best time to try petting them is when they're satisfied. That is, shortly after they're completely done eating a meal or 10 minutes or so after heavy playtime (too soon after playtime and they may see your hands as tasty chewtoys).
Start small, let them sniff your hand before touching them, keep the petting sessions short. Some cats can get overstimulated and bite if they're not used to being petted (this happens with my feral). If you're able to do this small amounts (and reinforce with treats) I think you'll see them seek out comfort and affection after a time. They may never be a truly cuddly cat but I do think that most ferals (particularly young ones) can come far enough to want human interaction and affection if they get it in the right circumstances.