Hit point loss is MUCH easier. You only deduct/add HD*X, where X is the difference in modifiers.
Skill point loss/gain is far more difficult, particularly for the DM. First of all, I doubt there are that many DM's who actually closely monitor the PC's skill ranks. More importantly, why don't you let the PC decide what ranks he gains? Can't he use fox's cunning to gain a few ranks in UMD for a moment or two, even cross-class? That's the absolutely best use of that house rule, and you don't allow it?
Do you, say, suddenly strip a full skill, like Tumble? That's really harsh, especially when the rogue tries to Tumble, and then . . . what happens? Technically, he can't even try 'cause he's untrained. It's really undefined, though I suppose just having it fail is acceptable.
I really don't like the twist with the hidden skill point loss/gain.
Btw, you obviously seem quite capable and competent enough to do it on the fly. I salute you for it. I'd personally rather use that extra processing power for something else. Specifically, I think 30 seconds can bring an exciting, tense combat to a screeching halt. IMO, if it takes more than 5 seconds, it's too long. If it takes you 30 seconds for one PC, it would take a lot longer all the PC's, NPC's, etc. in some special situations (like AMF, or area dispels, mass fox's cunning).