In hindsight, this was a head scratcher, but lets look at it from Kirk's perspective in real time:
2nd and 2 - Kirk assumed we could run for 2 yards to move the chains, stop the clock, and have a 1st and 10 from the ISU 20. Not the most aggressive call, but not terrible. I also assume we can run for 2 yards against ISU at will.
We only got 1 yard. 2nd timeout called with 40 seconds left. Obviously calling the timeout is a good decision.
3rd and 1 coming off a timeout. Kirk assumed we could run for 1 yard, stop the clock, and have a fresh set of downs from the 20 to try something. Maybe he even had the 1st down play called already. Again, this is conservative, but I don't think its terrible. We got stuffed, loss of 1 yard.
So now the clock is running, its 4th and 2, and I think calling a timeout with 2 seconds left is the right call.
Up until this point, I don't think you can really 2nd guess anything Kirk did.
The fake FG was the weird call. It got 16 of the 22 needed yards for a score, and I think I would have taken the 3 points, but whatever. It was fun, it was gutsy, and the team came out fired up in the 2nd half. Maybe that play contributed, maybe it didn't, but you're trading a high chance at 3 points for a slim chance at 7.
The thing I'm disappointed with on this set of downs is that 2nd and 2 and 3rd and 1 we couldn't run for a first down. That should be almost automatic, especially with 2 chances at it.