Good on you for going back to a snaffle, that is absolutely the correct thing to do in this situation. For now, I would lay off the neck reining, as you know she has a few holes in her training and those need to be addressed first, later on after they are filled I bet you'll find that her neck reining has improved because of it.
In order for a horses stop to be bad there needs to be resistance to the bit. To fix that, go back to getting her soft to one rein.
If she doesn't know how already, teach her how to flex. I start on the ground first and slide my hand down the rein, picking up very softly ( grab a couple hairs and apply some pressure, if you pulled those hairs out you are pulling too hard) and wait for two things, for her to stand still and for her to give to that pressure. She might lean on it at first or move around which is perfectly normal. You want to make sure you are just holding that pressure, if you need to brace your arm against your side so you are at a stopping point and don't continue pulling do that. Once she understands how to get off the pressure you want it correct, you don't want her just cocking her head way to the side and only bringing her nose toward you, you want softness through the whole head and neck, bringing her head around evenly.
You also want her soft through the body. How is she about moving her hip, ribs and shoulders around independently?
To get a good stop, I bend to a stop a lot. As in, I bend to a stop for a couple weeks, never picking up on two reins to stop. I don't use two reins until one is soft. When I bend to a stop I slide my hand down and bring my hand out slightly to the side. You are not yanking her around to your knee, pick up and wait for softness. Start this at a walk and as she comes to stop, slide your leg back and disengage her hindquarters. Once she understands how to do that softly without dropping her shoulder or running it out start getting her to respond to your seat. I practice it from a trot mainly, ride around, ask for that stop then bend down.
Once she's soft through her body and on one rein you can have both reins back again. Teach a good backup to introduce the correct response to two reins. Flex each direction first ( this should be super soft at this point, you should be able to just pick up a rein and get a response), then take the slack out of both reins and just hold, using the same pressure when teaching flexing. As soon as she gives vertically, you give. It doesn't matter if she puts her head up half a foot ten lowers it a centimeter, give then. You want to get her to understand that before moving on. From that point you can get pickier, lots of horses get the head down then move on to trying to put their nose in the dirt or hiding behind the bridle, at that point don't release until she breaks at the poll without over flexing. The third step to backing is getting an actual step. Once she gives nicely, keep holding and wait until you get a good step back. You want to feel her lift her shoulders and back a bit as she back up. Every time she does the right thing, release the pressure.
I spend about a week doing a lot of backing up before I ever ask for a stop. Not a lot of steps in a row really, just getting the steps I do ask for excellent. Just like everything up to that point, it's baby steps preparing the horse to be soft and to understand the next step.
Now you can actually stop. Start from a walk and just take the slack out, using the same pressure you have been to get a back, no more. Wait for the stop and the shift of weight. Then ask for a step back. Once the stop at the walk is good, move to the trot etc.
You're thinking, my god, why spend all that to just get one thing better i'm sure. However, everything i'm describing is going to get you that much of a better broke horse. However, that stop, is going to be great. You're getting your horse prepared to ride into the stop and stop correctly, not with the head up and back hollowed. You'l also find that when you move onto each step that the horse picks it up very quickly because it's prepared and there is no fight.
A good example of how all of that prep work is a mare I trained a couple months ago. I was getting quite a lot of flank for the way I was teaching her and I wanted to make a pretty big point. I asked this little mare to pick up a lope, towards her pasture, I sat down and closed my fingers on the reins to take the slack out. This was a green mare, who I had NEVER used two reins on before outside of backing up. She melted to such a nice little stop and was prepared to back up. I had kept hearing "she's been under saddle for over a month why haven't you stopped her normally yet." and my friends just were not getting it, my point was that when I DID finally ask her to stop, she would be prepared to do so, because at that point she was soft backing up and had an excellent stop off of my seat. Would I expect the same response out of every horse? Heck no but with how soft through the body and face she was at that point I knew I could skip a few steps to make that point.
At that point by all means, neck rein again. At that point she'll be soft enough in mind and body that I think it'll be a lot better and if you need to need to correct with your legs or pick up and direct rein that will be softer too.