The Australian led most of the race, only to develop an arm pump problem which slowed his pace and allowed both Yamaha's Jorge Lorenzo and his team-mate Dani Pedrosa to slip past into first and second.
Having suffered and rectified similar problems in 2010, Stoner says he is confident the work done since Qatar will ensure there is no repeat of the arm issue this weekend at Jerez.
"Since Qatar I've been working on the arm pump issue I experienced in the race and it's definitely feeling better," Stoner explained.
"We've treated it the same way as when I had it in 2010 at Silverstone so I'm hoping it won't be a problem for us this weekend."
The reigning world champion said he was also hoping Honda could improve its chatter issues at the Spanish circuit.
"We still have some issues that we really need to resolve with the bike, especially the chattering in the entrance and exit of the corner," he added.
"When we solve these we believe we will have a very competitive package.
"After a difficult race in Qatar, I'm looking forward to Jerez. We had a very good pre-season test there, it's a track that hasn't been so good for me in the past so the fact we were able to hold a good pace there in testing has given us a lot of confidence."
Stoner's team-mate Dani Pedrosa said he would be targeting an improved qualifying performance at Jerez, having lined up on the third row in Qatar.
"We need to be very focused and have a good qualifying session in order to start the race in a good position," he said.
"We had a great race in Qatar and to start the season on the podium is important, but we cannot relax, we will be aiming for another strong race this weekend."