Ouch. I think at some point I did something to permanently lower my Two-Handed skill.

If you think this is not true and there's an alternate reason (or possible solution) please tell me.

I, much earlier, trained Two-Handed to 34, then Sergio gave me an additional 2, bringing it to a total of 36. I equipped a Two-Handed weapon named something like "Enchanted by Ulthar" which boosted it by an additional 4 points.

Later, after reaching Jharkendar I sold this weapon and got the Typhoon from Cronos, which boosts it by 5 instead.

... Now that I have my Magic Wand (does not affect Two-Handed skill but boosts mana) equipped I glanced at it and was surprised to see that it is now 31.

So my current theory is that somehow I equipped Typhoon without it boosting my skill so when I unequipped it it permanently lowered it by 5 instead!

:( No recent saves either, gonna have to live with 5 lower 2H skill than I could have had.

Well, this could be either what you think (that you equipped Typhoon in a buggy way), or... The most basic question: have you had Marvin Mode enabled anywhen during that?

You've probably equipped Storm/Wind Cudgel, which decrease the 2H by 10%, while using Marvin. Marvin is known to bug with attribute/skill-boost items. For instance, if you have STR 50 (Marvin enabled) and you equip and unequip a belt STR +5, it's possible that your strength remains (EDIT) 55.

Anyway, you can change it with Marvin, either by adding yourself 5 LP (through Edit Abilities), some gold and learning it again from a teacher, or directly by adding 5% to your weapon (2H) proficiency through Edit Abilities -> Hitchance.

I had a similar problem and managed to confirm that it was caused by polymorph spellcasting. When you return to human form the game arms you with the best weapons found in inventory (meaning the ones that are listed first), which may be different from what you had armed when polymorphing. So, I was using Beliar's Claw (no skill bonus and 99 damage) while having Master Sword in inventory (+10% skill bonus and 120 damage). When returning to human form game was arming me with Master Sword, without raising the skill, so that when I was switching to Beliar's my skill was dropping by 10% (interestingly the moveset didn't change even though I dropped below 60%, which made the bug more difficult to spot).
Best solution I came up with was to use marvin mode to give myself some stat-increasing stone tablets:
"insert ItWr_OneHStonePlate1_Addon" (for two handed "Two" in place of "One").