Assuming you can complete a planing gybe the best way to improve alpha speeds is to improve your cross wind speed and sail to the maximum of the 50m proximity.
In choppy water this probably means making sure your FSW straps are in their outer positions and getting a good pointer (slalom) fin.
Weed / wave fins are much harder to get a good cross wind speed with in choppy conditions.
Sail needs to be rigged a bit flatter than you would for down wind speed with a bit less downhaul (cammed sail). Wave / freeride sails will be easier to gybe but not have as much acceleration out of the gybe or stability in gusty conditions cross wind.
Try and sail 90 degrees to the wind, gybe in to the gust not as you come out of it, head slightly upwind to wash off a bit of speed and gain some upwind ground before gybing and go as close to the 50m max proximity as you can.
If you have the space start your alpha run at the end of a downwind run to build up speed then harden up to 90 degrees trying to keep as much speed as possible
The track of an alpha probably tells a clearer story. A 20Knot alpha with a 25 knot peak (if it is off the wind) is a good result in choppy conditions.
If you are analysing using software (examples from Realspeed) look at the track and speed.
look for a steady incoming speed and a quick return to speed. This example is probably not 90 degrees and was slightly downwind on the way in and upwind on the way out.
Here is a track showing a smooth gybe making the 50m proximity (circle) but could have been slightly more square to the wind on the way out to graze the circle. This is very difficult to do without some kind of marker or doing lots of gybes and hoping you luck one.