Probably, if you were doing this on Linux, you'd follow someone's Linux tree, and not run Debian unstable with updates to everything.

You might end up building a lightweight distribution yourself; some simple init, enough bits and bobs for in place debugging, and the application and its monitoring tools.

Anyway, if you did come across a problem where userland and kernel changed and it wasn't clear where the breakage is, the process is simple. Test new kernel with old userland and old kernel with new userland, and see which part broke. Then bisect if you still can't tell by inspection.