In addition to the above suggestions, if you don't have a splint, try to avoid hyperextension of your MCP and PIP joints when applying deep pressure. Keep the joints neutral/slightly flexed and use other digits to support the "mobilising digit". Apply pressure with the pad of the tip of the thumb and not the volar surface of the PIP which I think may be a common mistake.

Also change thumbs and/or fingers while mobilising soft tissue. Give those fingers a break.

I don't really have pain in the joints after mob'ing soft tissue but my intrinsic muscles turn to jelly afterwards and my hand-writing (bad at the best of times) becomes attrocious!