I'm in the same boat when I'm in Serbia and the Balkans shooting some pretty ancient frescoes, some quite marginal.
I'm now using a pair of D800 bodies and have changed my lighting technique from flash to using a small high-output LED spot, a Lenser AAA powered light. The modern icons, I'll light but the old ones need to be done carefully. This allows me to gently light the icon and paint larger panels as needed. It's mainly used to highlight and emphasize a particular writing.
When I can, I'm using a tripod, etc. but sometimes, I've got to wing it and crank up the ISO.
Getting a good exposure is key when you can. I am not using IR since I'm trying to document and slightly enhance the original work.
However, the magic happens in post processing. Don't be afraid to push the sliders in ACR. Sometimes that will pull out some of the hidden detail. Next is to do a b&w conversion using Nik Silver Efex. It seems weird to do this to enhance the color, but stay with me. Sometimes, you need to change the filtration at this point. Nik gives you a box of Wratten filters that allows you to simply click the color and push the slider. This may get you in the IR range without having a converted body.
My goal here is to get a b&w image that converts well and has some contrast and "pop". Mostly, a canned preset is all it takes me here. When it looks good, let Nik do its thing and you'll have a b&w layer over your color image. Next change the blending mode to "Luminance". The contrast and detail should really pop. However, sometimes the image seems a bit flat. To counteract this, I add another Vibrance layer with both the vibrance and saturation pumps up +20 to 40 on both sliders.
I've used this technique to push certain images that I could not easily go back to rephotographed and comparing the processed with the raw image is really something to see. The original raw captures simply seem lifeless and flat. Once processed, the detail comes out and is amazing. It may not work for all your frescoes, but it may be what may work.
I don't have any examples on this computer but I do have them in my studio. I'd be happy to show you off-list if this may help.