That improvement put the young Ducati Marlboro star almost a full second inside Valentino Rossi's fastest race lap from last October's Australian Grand Prix - which Stoner won - and kept him comfortably clear of the competition.
"Today I set my fastest lap on tyres that had 22 laps on them and that is really positive because it means that the modifications we tried on the set-up have had the desired effect, which was to increase tyre durability. This also allows us to consider using softer tyres, at least in the odd race," said Casey, whose best time was also four tenths inside the 990cc circuit lap record set in 2005.
"This morning I went out twice for just 5 laps each to verify engine response, which is now smoother at the bottom end; everything worked brilliantly and I'm really pleased. The track conditions were never perfect but with some changes to the rear suspension we were able to set some fast times, all of them on race tyres.
"I think it will be possible to repeat those times in the race here too because the new Bridgestones are even better than the ones we used last year. Hopefully the weather is good tomorrow so that we can complete a race simulation," he added.
Best of the rest was MotoGP rookie Alex de Angelis. The San Marinese had been an impressive third fastest on day one, behind Stoner and Colin Edwards (qualifying tyre), and the Honda Gresini rider matched Stoner's rate of progress to remain half-a-second behind the #1 after day two.
A further 0.6secs back was another former 250GP star riding a satellite Honda, in the form of Andrea Dovizioso (JiR Team Scot). Due to the rain, Dovizioso - like almost all the riders behind him - lapped slower on Thursday than on day one.
de Angelis' veteran team-mate Shinya Nakano took fourth position on the second Bridgestone-shod RC212V while Nicky Hayden, the only factory Honda rider present following Dani Pedrosa's Sepang injury, moved from eighth to fifth after almost exactly matching his day one pace.
The third MotoGP rookie present, Yamaha Tech 3's James Toseland, slipped from fifth to sixth on day two - 1.5secs from Stoner - but outpaced team-mate Edwards by 0.1secs and four positions.
Sandwiched between the two Yamaha YZR-M1s were Marco Melandri (Ducati Marlboro), Loris Capirossi (Rizla Suzuki) and Randy de Puniet (Honda LCR). Melandri had also been a whisker slower than Toseland on day one, while Capirossi improved by two places as he and team-mate Chris Vermeulen (11th fastest) continued to try and crack one of Suzuki's worst tracks.
Anthony West was the top Kawasaki in twelfth place but team-mate John Hopkins was left at the tail of the timesheets after falling - and injuring his groin - while riding in the wet. Hopkins went to hospital to get the injury checked and it remains to be seen if the Anglo-American can return for Friday's third and final day of testing.
Between the two ZX-RRs were Alice Team riders Toni Elias and Sylvain Guintoli, who may have been left over two-seconds from Stoner - but at least joined the Australian in improving on their day one best.
