We have very similar jobs (though I don't make jewelry in my free time). There are benefits to working for NPO's, but you're right that even NPO jobs have limitations on what they will put up with.
I'm not sure what kind of pain you have. I have pain in my low back, radiating down right leg & in my neck/shoulder/base of head radiating down my right arm. If the pain is in your upper body, try adjusting your seat, getting something under your feet if you're short & making sure your stuff is all within easy reach. That means your monitor is 12" from your head & the top of the screen is at eye level. Your phone (if you use it) is within easy reach of your computer. And, if needed, maybe look into special technology. I just got a Goldtouch keyboard (it's fully adjustable -- go to the site, I really can't describe it) and have an Evoluent vertical mouse on order (GT sells them, but they're manufactured by Evoluent). You can get them used or remanufactured to save money. Goldtouch sometimes is really nice to NPO's with pricing, but it depends on what time of year you're ordering. If they can't give you a good price, ask around.
If the pain is in your low back, make sure to schedule breaks (actually, that's just good advice no matter what). Sometimes I've used a balance ball in place of a chair. I've gotten mixed results from that. At my current workplace I have an office, but at the NPO where I used to work I had an open cube, but I talked to my boss & she set it up so I could borrow an office or meeting room for 30 minutes basically whenever needed so I could lay on the floor & stretch out my back. I also talked to the cafeteria manager & was allowed to keep an extra large ice pack in the freezer (the kind that are 24"x24" -- they sell them at Walgreen's & other pharmacies; they stay cold for up to 8 hours, well, I've only gotten them to stay cold for 6 but they say 8 on the package). I switch positions a lot -- sitting, standing, walking around for a minute, kneeling on my chair, sitting sideways, sitting backwards. I also, on occasion b/c you can't use it all the time or it will make you worse, use a cervical collar for neck pain and a hard prescription back brace for low back issues.
And then at home (when I'm good & I've been naughty lately b/c I'm trying to pack to move) I do crunches -- regular up & down, but also the sideways ones & the ones where your top half stays flat & you reach your legs/toes straight up in the air. Plus I got a home traction unit. It's under boxes right now (oops) but it did help a lot when I used it. My insurance covered it 100% b/c I had met by out of pocket max.
Other than those kinds of self-care tips, I would say to try to find some powerful people to get on your side (donors are the best, board members are also good). If you can show that you have strong people skills & that people who give a lot of time or money to the organization, or people who are very powerful in your field, are wanting you there then your boss will find a way to accommodate you whether he likes it or not. I know I hate the whole political aspect of universities & higher education groups, but it can literally mean the difference between having a job or not. Find those people & if they ever send you a letter figure out how to send them a nice response & copy your boss on it so he knows that people like you & will be up in arms if you leave. Higher Ed can be a double-edged sword. I remember even when I was in school it was like that. Now I'm starting a new job & was told I had to be the gopher for our semi-annual conferences. But I make nice with a few people who brought in a number of new members because of me & also the top person in the field. They threatened to leave the organization & to tell everyone they knew how unhappy they were if my boss didn't figure something out so that I didn't have to be on my feet all day long at conference time. God bless them, they even offered to run errands for me (and these are well respected professors & authors of some of the leading textbooks in the industry).
I know sometimes that's easier said that done, but I've also seen that often people with pain/disabilities are the most sensitive people out there & are really good at customer service. So pull out that roladex & see what you've got. :)
Gosh, sorry for such a long post. It seems like trying to stay on top of the pain so I can work 35 measly hours a week is like a second full time job, but most of the time it does work for me. And the rest of the time, I make sure I'm building relationships with the important people. And I'm really evil & sneaky b/c if I'm going to be out I will send out an email to those key people letting them know that I'm home & available on my cell if they need me so not to worry about bothering the boss (as nice as they are, they can turn on you in an instant so I take every precaution). At every organization I've worked for that always seems to result in them mentioning how helpful I was even while out sick to my boss. Gotta love that. :) I really try to keep that group as small as possible -- no more than 6 people -- but it does seem to make a difference. I help them; they help me.
Hope that helps. Wishing you favor with your boss, relief from some of the pain & steady work for years to come.