Seems to me you're cherry picking your test results.
The fastest P-39 was the N, clocked at 398.5.
A graph in wwiiaircraftperformance shows a P-39Q-30 without wing guns at 410mph at 10000' and 400mph at 16000'.
The fastest A6M couldn't hit 360, even the versions with increased HP.
And the A6M had a very hard time maneuvering above 300; those big ailerons were very hard to move.
The problem the P-39 had in the PTO was in large part due to the USAAC being at the bottom of the learning curve in tactics and maintenance while the Japanese were experienced in both.
Agree, they had experience in China.
The Japanese had their logistics worked out, the USAAC did not.
True, AAF had a hard time maintaining their planes. They got better, but it was rough in 1942.
The P-39s were often sent up to intercept Japanese bombers flying at 20,000 ft. It would take 6-8 minutes for a P-39 to reach them, by which time the bombers would be gone. Meanwhile, the climbing P-39s would be bounced by A6Ms.
Try reading P-39/P-400 vs A6M3 Zero New Guinea 1942 by Michael John Claringbould. It has some good combat accounts, some of which will say the P-39 and A6M were close in speed, some were the P-39 was faster, likely due to acceleration being close for the two aircraft. But the main reason to read the book is the in-depth look at combat records; the P-39 and A6M were even in the win-loss stats. That surprised me.
Especially with pilot quality, the Japanese were experienced carrier pilots, the Americans just out of flying school. Some didn't even have any fighter training. Smart kids, they learned fast.
As for the A6M having a service ceiling of 35-38,000 ft, that didn't mean that it fought at that height.
Right, service ceiling was largely a test number achieved under test conditions.
Service ceiling means the rate of climb is 100 feet/minute.
Better measure is combat ceiling where it would no longer climb at 1000fpm. Hard to climb at less than 1000fpm in combat.
A6M performance fell off at 20-22,000 ft, like the P-39's did at 18,000 ft. That 2-4,000 ft made a difference.
With a little less weight (300lbs or so) P-39 would climb with a Zero.
Also recommended is this December 1942 comparison report between the A6M-2 and various US aircraft including the P-39D:
http://www.wwiiaircraftperformance.org/japan/intelsum85-dec42.pdf