If it pulls to 5200 in 2nd but won't pull to 5200 in third, talk to your chip maker. There may not be enough timing in 3rd gear.
Also, switching to 28" tires won't hurt your car at all and can only help.
My car has way less mods than yours and has run 8 mph faster. I won't run anyting but 28" tires, even on a stock car. Prepped track or no, they are always easier to hook than 26" tires.