Marquez's pre-season has been hindered by his ongoing recovery from a shoulder operation in November, though he admitted after a difficult Sepang test that he was more worried about the bike than his injury.
Honda's woes, mainly surrounding corner entry and poor turning, continued on the first two days in Qatar, with LCR's Cal Crutchlow revealing he was having to ride the bike like an "amateur" just to stay on it.
Honda was so worried that Marquez was given one of LCR's Takaaki Nakagami's 2019-spec bikes to try on Monday's final day of the Qatar test.
After trying various parts, Marquez said he thinks Honda has found a way forward with its bike.
"We found the way," said Marquez, who was seventh fastest on Monday.
"In Malaysia there was some problems that I didn't understand, some strange crashes in the fast corners that normally I'd save but I was struggling a lot, and [on Sunday], again, another strange crash.
"Maybe I'm thinking always about my physical condition, I say, 'I'm riding the same like always', but then I saw that all of the [Honda] riders were struggling; not only my team-mate, who is a rookie, but also Cal.
"I want to say thanks to Honda, to all my team, to all my mechanics because they did a great job.
"They concentrate all the power and all the effort inside my box and we found the way.
"I was riding very good, we understand many things, we tested some 2019 parts to try understand where was the problem and we found the problem.
"This is the most important thing of the pre-season, because yesterday [Sunday] we were very far and I was not enjoying riding the bike, and today I enjoyed it and we were much closer.".
Asked if Honda had made progress with turning, he said: "We were missing the front feeling.
"The entry of the corner was not good, and then we didn't have the speed of the turning.
"And then we tried to recover the grip on the exit - the speed that we lose on the entry - and then we lose the grip.
"The entry improved, mid-corner improved, so exit was faster.".
Marquez tried last year's Honda aerodynamic fairing (pictured above) on his 2020 bike on Monday, and retried a chassis he had previously tested but found little gain with.
Now Honda has found a set-up direction, Marquez said it will have to retry many things in the coming race weekends.
"We tried a different chassis too at the end of the day," he added.
"The problem is all the work we did this pre-season was not working and... we start in one point, we try many things, and we finish in the same starting point.
"So now that we found the problem, we need to retry all the things.".
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