The 14-year-old endured a tricky weekend at Oulton Park in Cheshire as changeable weather hit the races but the FPW Racing rider still managed to secure yet another double podium.
The championship fight, however, is over after Jake Archer wrapped up the title with a round to spare.
Third-placed Jack Scott also moved to within 11 points of the Eccleshall teenager following his double win over the weekend.
Team manager Adrian Mason said: “The weather was extremely changeable all weekend and luck was not on our side.
“Storm had an unfortunate crash in FP1 in end FP2 in third position, with both sessions taking place in wet conditions.
“Saturday’s qualifying was again in mixed conditions but with a drying track the team chose the safe option of wet tyres.
“With Storm regaining his confidence from Friday’s crash he qualified in ninth position.”
Light rain began to fall at the beginning of race one and, with many riders on slick tyres, race direction brought out an early red flag to allow a restart on wet tyres, if preferred.
With more intermittent rain, FPW Racing opted to run rain tyres and a full wet suspension setting, despite the track drying in places.
After a good start from ninth, Stacey was unable to catch Archer, Scott, Dan Jones and Brandon Pasche on the first lap but refused to give up and eventually managed to claw his way back up to third.
A drying track on Sunday meant Stacey started the second race with a slick rear and wet front.
And the move seemed to be paying off as he took the lead from fifth and crossed the line in first position for the first five laps.
But with the track drying he was unable to make a larger enough break and was eventually reeled in by Scott and Jack Nixon, who were on slicks.
Stacey’s form this year has been so impressive he will be taking part in the Red Bull MotoGP Rookies Cup, which takes place between October 1 and 4, after competing in the British Talent Cup next weekend at Assen, in Holland.
He will complete his British Motostar duties at Brands Hatch, in Kent, at the meeting being staged from October 12 to 14.
Team manager Adrian Mason said: “A few British riders have been invited to the test – including Storm, Josh Whatley, Harry Leigh and Ross Maguire.
“They have a signing on Monday, initial trial on Tuesday, day off on Wednesday and those that have got through have another trial on Thursday.”