Like Francesco Bagnaia and Joan Mir, the Repsol Honda riders must now hope the Mandalika circuit is dry tomorrow morning to have any chance of breaking into the top ten.
Although Marquez fortunately walked away from his accident, bruises showed how big the impact had been.
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"I felt better before the crash! We will see tomorrow morning when I get up," he said.
"Overall I’m happy with the day, but it was not the time for a crash and we cannot be happy because we are out of the top ten and that was the target.
"Anyway, now it’s time to pray for dry conditions tomorrow morning and try to be in that top ten."
Fifth in the Qatar season-opener, Marquez continued his quest for more front-end feel from the new Honda.
"We changed a little bit the set-up in my direction in FP2 especially. It looks like that front confidence is coming better," he said.
Instead, it was the rear of the RCV that seemed to be causing Marquez issues, the Spaniard fighting some big slides.
"I think it’s more the character of the rear tyre," he said of Michelin's change of tyre casing this weekend, in response to the formidable Indonesian heat. "There is much less grip and less warning."
With the latest RC213V designed to generate more rear-grip, Marquez admitted it was a concern to feel the rear 'floating' but certainly not 'a disaster'.
"We need to understand where that floating is coming from on the rear. But it was not bad. I was able to ride well. It didn’t help to have a constant pace but it wasn’t a big disaster," he explained.
"This morning we were there with the medium tyre, before everybody put the soft. Let’s see if tomorrow we can improve and show our speed.
"The medium is an option for the race but the question mark is if the soft is an option for the race. That’s the question mark. We will try to understand tomorrow but the choice will be between the medium and the soft. Let’s try the soft and we will see how the endurance is."
Speaking separately Espargaro, fastest in February's test and again in the damp FP1 session, explained that he had been hindered by a front brake issue on his final run leaving him 19th. But is otherwise 'comfortable'.
"In the morning with the dirty track and the medium tyre I was able to set the fastest lap time and in the afternoon I was around the top five so I feel OK. The bike feels very good both with the soft and the medium tyres," Espargaro said.
"I didn’t change anything [from the test] but I had the front issue on the brake. I had no front brake on the last run. I was angry because if it rains tomorrow we are not in the Q2.
"But we have many parts on the bike and that can happen. It is a technical thing and important to understand so it doesn’t happen in the future.
"I am fast, we have good speed and the bike is working good. We have good grip with both tyres and enough to make a lap or good rhythm so I feel comfortable."