Attack speed is not desirable on many tank junglers anymore because they usually won't be taking Machete first. Mpen is fine. Otherwise just take flat AP or AD.
Just to expand on this, the jungle tanks where AS marks are still the better option are the few who have on-hit effects (e.g. Nautilus).
I can't decide on the right Sejuani runes and masteries.
For runes Hybrid Pen or Magic Pen marks? Feels like Hybrid would be better for clears.
Flat Armor or Scaling Health seals? Her W does scale with health...
CDR or MR Glyphs?
MS, AP or Armor quints?
Feels like anything and everything sorta works.
With Masteries I'm switching back and forth between 6/6/18 and 0/12/18.
Any advice at all? I really like playing her in the jungle for all the CC.
Everything you've written down is fine. If you happen to be doing better with X than Y runes despite what other players recommend and what the data shows then stick with that.
Generally speaking, tanks have been moving towards either penetration marks (hybrid, magic, or physical) or armor marks, but lots of players still prefer attack speed. Even though it might not be the best choice damage wise, it does clean up some champions' auto attacks and makes them more user friendly, although if you stick with one or only a small handful of champions you'll eventually get to know their little idiosyncrasies such as how their AAs feel anyways.
The most general tank rune page is something to the effect of penetration marks/health seals (scaling or flat, or even a mix)/scaling CDR glyphs/armor quints. Some high level players change things up a bit. Valkrin for example likes to stack all his glyphs as flat CDR and use one CDR quint to start the game at 10% CDR.