I would suggest using that $200 voucher to do a mileage run from SAN to PBI/SRQ/TPA/JAX. I've seen many of these availble in the range of $198-$240 pre tax. With very little out of pocket, that's close to 5k EQM. You can possibly get more out of it for routing through ORD or adding connections through LAX/MIA etc.

Aside from the glitch causing the delay, not sure I would persue anything...you did get F for coach price and the voucher, and when you agree to take a change, there's always a small risk of glitches.