If you get sore in the prone (or any other position) it means you're muscling the rifle. If you're muscling your rifle, you have a poor position.
I've found that using a pillow or a blanket folded up and tucked under my chest eases the strain on my neck.
Adding pillows and blankets do not fix the problem, it mast the problem. You need to fix the problem. I know many here are dead set against the "cocked leg" position, go ahead and trash it, but you cant dispute the fact it takes pressure off the stomach and diaphragm.
You have the pressure or discomfort that's indicated, they you are going to subconsciously or even consciously adjust your position to relieve the pressure that's causing the discomfort; that means muscling and muscling means fatigue.
If you have back-neck problems that cause discomfort then find a coach that knows how to deal with disabilities to help you find a position that works for you. There is no law that says prone or any other position cant be modified.
When my wife was activated and deployed in 2003, she couldn't shoot prone because she broke her back coming off a colt in '99. I was at Bening when she was processing. Of course being retired I wasn't allowed on the range. The qualification required shooting from the prone so I talked to some cadre about her problem asking them to find some one who knew something about coaching and disabilities, they did and he found her not only a position that worked for her, but allowed her to shoot expert. She broke her back again while deployed and now has 3 rods between her shoulder blades. Not a lot of movement, but I can get her to shoot prone without discomfort.
To me, watching people shoot while flopping around like a chicken with his head cut off grates me like fingernails on a chalk board, but you see it at every range. Then you see others who don't seem to move at all. If it wasn't for the rounds going off you'd think they were sleeping.
As to recoil: Brakes work, yes, but again its mast the problem instead of fixing it. Laying down behind a rifle that's resting on sand bags fore and aft, does nothing to control recoil. However, if you were to property use a slung position, the recoil is distributed through out the whole body and not just the shoulder. No law says you cant use a sling with sand bags or bipods (except in the CMP Vintage Sniper Matches, you can use a sling or bipod but not both). Try the sling with your bipod or sandbags.
When you get into a prone position, totally relax, dropping into a total relaxed comfortable postilion, using no muscles, close your eyes and relax. Now open your eyes and see if the sights are lined up. If not, then adjust WITHOUT muscling. If your off windage wise, pivot on your belt buckle, if its elevation, then adjust elevation by sliding the support hand fore and aft on the stock or if you're using sandbags or bipods adjust them accordingly. The close your eyes, fall back into a totally relaxes position, open your eyes to check your NPA, if its off, repeat the above process.
Too many people know what they are suppose to do, but instead of correcting the position, they get lazy and muscle the rifle to push the sights on the target. Muscling. You're right back where you started.
There are some great DVDs out there, Franks has some, Rifles only has some, as do others. They point out what is suppose to be done, but the authors of the DVD's don't watch you shoot to see if you are following their instructions. If you can't find a comfortable position on your own, then find a coach who can.