Are your rudders locked all the way down and is your helm balanced? The first thing that comes to mind when someone says their boat won't accelerate in a puff is rudders being out of balance. You should also make sure you have the rudders on the correct sides of the boat and measure your toe in/ toe out.
Rudders on the correct side of the boat? I thought I was certain that the rudders and daggers were symmetrical?(!) I've got a bushing kit on the rudder pins and nylon washers on the rudder bolts, I also put some waterproof duct tape on the old-style castings I have to brace my plastic rudders... I've adjusted rudder rake to a weather helm and everything locks down like it should (I even used the hobie print-out template!) I have the rudders aligned within +/- 1/8" from the center of leading edge to the center of the trailing edge, though they are plastic and have some slop.
Do you have a bridle vane or another way to read apparent wind?
It may be that the gusts are coming at you from an angle different than the wind.
I have yarn on the bridle... I think I should buy that bridle fly though...
the gusts are actually headers.
Yes! I payed attention today and noticed huge headers... I have to be way more aggressive on the tiller on days like today I think. Yesterday I was sheeting in to "power up in a gust" that was actually a header instead of falling off to catch it...
Optimum upwind angle for a Hobie is 50-60 degrees true wind (or ~30 degrees apparent wind), again depending on your mast rake, weight, weight positions and a whole slew of other factors. Most of it is based on "feel" of the tiller, as you seem aware, so you just need to sail a bit more to get a feel for it. Experiment!
Mast rotation shouldn't have any effect here, it's primarily used to control the fullness of the mainsail and the sail entry to the wind.
I logged a 12 mile round trip today (moderate wind, but not able any reaching in the narrow bay... lots of tacking and jibing) in about an 1h15m and played around a bit... I think you are right, I'm just pointing too high: I've been trying to target within 45 degrees off the true wind. I'll have to go look study the polars... I glanced at them once in that hobie U document, but didn't pay real close attention. I'll make sure I'm at least 50 off the true wind until I get my senses adapted.