"We're down on radar speed, and acceleration mainly [even with the spring-valve engine]," he continued. "This week I didn't make a jump with qualifying tyres, as I would have liked, but I think generally I feel comfortable on qualifying tyres and they help our bike with acceleration, due to the extra corner speed."
Hayden believes it is unlikely that the spring-valve engine will be improved further, since all efforts are focused on bringing the pneumatic-valve engine up to speed.
"I'm not sure the spring-valve engine is going to get a lot of development from now on; it's hard to develop both engines," he said, when asked if the two designs could be developed simultaneously.
With just two more tests before the season-opening night race, Honda is facing a difficult decision in terms of which chassis/engine set-up to concentrate its immediate future on - and Pedrosa's injury has clouded the issue further, since the 2007 world championship runner-up needs to ride the latest version of both bikes to form a full opinion.
As such, a final decision only looks likely after Pedrosa's return to action, which the Spaniard hopes will take place next time out at Jerez, from February 16-18.
The official Jerez test might see the pneumatic-valve engine return to action, and the Spanish appearance is expected to be make-or-break in terms of whether the powerplant is raced at round one.
"Before I would have said 'yeah sure, we'll race the pneumatic-valve', but now maybe we're going to be on valve-springs [at Qatar]," admitted Hayden. "I don't want to commit one way or the other at this point."
But one thing that isn't in doubt is the effort Hayden and his team have put in to try and improve the situation.
"All I can do is ride the bike and focus on what I've got," reflected Nicky. "I think the bike will be all right. We'll see. We'll know a lot more when we get to that first race. We've made some progress, but for sure our rivals look real strong now, so we've got a lot of work still to do if we want to be a contender.
"My guys are working really hard. Everybody says 'it must be so hard for the riders, riding around Sepang in the heat all day' but honestly we've got the easy part!" he smiled. "The team has worked really hard here - and I appreciate that - even though we've still got work to do. We'll just keep trying to chip away."
Pneumatic-valves already control combustion-gas flow for the Suzuki GSV-R, Kawasaki ZX-RR and the latest Yamaha YZR-M1, while Ducati uses its trademark desmodromic valve system - making Honda the only factory team still running valve-springs.