Saul is correct, use new or very good motor mounts. The Mazda comp mounts are the same price and fit just like your worn out stock units.
The 2-3 shift is tricky. As you prepare for the shift, your hand knows where 2nd gear is and anticipates where 3rd gear is. When you release the gas to shift, the entire drive train moves in the mounts. Which relocates 3rd gear to someplace your hand does not compensate for.
To cure this, let go of the shifter. Bump it into Neutral, then release the shifter. There are 2 small spring that will line everything up perfectly for a bump back up to 3rd gear. The bump/release/bump only takes 1/2 a second, but makes the 2-3 shift a reliable shift.
Other hints, use a stock shifter (required for SM) rather than a short shift kit. And, use the stock shift ball. The internal springs (mentioned above) are matched to the weight of the shift ball and the length of the lever.
Stock shifter + stock shift ball + bump/release/bump will make 2-3 shifts easy. (new springs help too)
Advanced Autosports, the nations most complete Spec Miata shop
Author, Spec Miata Constructors Guide, version 1 and 2.0
Building Championship winning cars since 1995
3 time consecutive Central DIvision Champion car builder 2012-2013-2014
2014 SCCA Majors National point Champion car builder
2014 SCCA Northern Conference Champion car builder, Spec Miata (Burdzy) and T4 (Bender)
2014 SCCA Runoffs winner, T4 (Bender)
2014 Central Division Champion, ITS (Wheeler)
2013 Thunderhill 25 hour winning crew chief
2007 June Srints winner, (GT1, Mohrhauser)
Over 200 race wins and counting.