...it being a radial and hence hard to cool....
Radials are very easy to cool. It only gets tricky when you want to minimize cooling drag to the absolute minimum, which they did on the B-29, and have ineffective engine cooling as a result. Bottom line was that the R-3350 was a new motor in a new aircraft and the kinks had not been worked out yet. There was tremendous pressure to get the B-29 airborne and combat capable as soon as possible. The R-2800 was fortunate that none of the aircraft designs (F6F, F4U, and P-47) that used it were really pushing the cooling system envelope when they were introduced. Don't forget that the B-29 was designed around a requirement that it fly from the U.S. to Germany on one tank of gas. The designers were looking for every single advantage they could, and obviously cut it too close on the cooling system. Ultimately, after the teething problems were solved, the R-3350 was one of the most successful piston engines, especially in airline service after the war. It was even used on a few fighters, and can still be found at Reno powering some of the Unlimited class racers.
And, the USAAF gun-decked the F4U test just like the Navy gun-decked the P-51D evaluation. Neither service wanted the other services aircraft forced on them just because the War Production Board thought it would be more efficient.