Naproxen

Have been taking 2 x 500mg of Naproxen daily for the last 15 months for arthritis in both knees. One knee was bone on bone, the other with mild arthritis but very painful through overcompensating.. After the first 6 weeks I developed horrendous indigestion but restarted them after a few weeks with lanzoprazole. Had tried various painkillers including coocodamol and tramadol but they didn't touch the pain and made me very sleepy during the day so as Naproxen was the only thing that had any effect [ took the pain from agony to bearable] I decided to stick with them despite the horrible things I had read. Had a left knee replacement 3 months ago. Was advised to keep taking the Naproxen during recovery as well as cocodamol. Recovery from the op was brilliant initially. Got mobile very quickly, back to gardening, walking, housework etc within a month or so albeit with some stiffness. Was able to come off the cocodamol at about 6 weeks. Here is my problem now. I have really taken on board exercising my new knee more and go to the gym 2x weekly, Aqua aerobics 2x weekly as well as daily walks of 20 to 40 minutes. Got a fit bit which really helps to motivate me. Time to come off the Naproxen I thought but I'm so disappointed. My knees still hurt, just differently. Although I can walk and exercise without pain, the minute I sit still I stiffen up and hobble when I get up till I get the knees working again. Don't get me wrong, the operation has vastly improved my quality of life. With bone on bone arthritis, walking for more than a few minutes was excruciating and I'm now able to enjoy walking again. At my final physiotherapy appointment I mentioned all this but they said it was quite common and I was doing well. It sometimes took 6 to 12 months to feel normal again.
Been off Naproxen 6 days now. The pain hasn't interfered with being able to walk or do exercise, but the stiffness and pain in bed has left me a bit deflated. Another thing I have noticed every time I try to stop Naproxen is that my IBS comes back immediately and I'm back to rushing to the toilet after every meal. I suppose it makes sense that an anti inflammatory would control bowel inflammation. So here's my dilemma: Do I keep on with the anti inflammatories because they are having a positive effect in the present or do I persist without them so that future side effects are avoided. My doctor is very vague seeing positives on both sides. I suppose I'm also a bit gutted that my operated knee is still stiff and swollen despite my best efforts. Has anyone been on Naproxen long term with no apparent long term damage? I don't know what to do for the best.