Could this be something tune related? You moved from Colorado which is a really high elevation to San Diego which you're basically at sea level. Fuel enrichment may need to be adjusted by your tuner.
with the MT-82, you don't want to try to force the stick into the next gear. Use the centering spring when shifting from 2-3. with an open palm push the stick straight up, because of the centering spring it will put you into 3rd automatically. The smoother and more relaxed you are the faster the...
this is totally normal. when I bought my '11 5.0, it got really bad mileage while the engine was breaking in. I believe it started getting good gas mileage after about 1500-2000 miles. went from 10-12mpg to about 21 mpg with mixture of city and highway driving with a few spirited sprints each...