The B-29 was fragile. It was SOP in the PTO on takeoff that if an engine had a runaway temperature, that the crew was to bail out. This may sound bit odd, but the B-29 had a few design flaws that resulted in catastrophic consequences. The first design flaw were the valves on the rear cylinders. They were subjected to much higher temperatures than the front cylinders. If the valves stuck open, this could cause a fire in a few different ways. Secondly, the magnesium accessories box mounted at the rear of the engine was a powder keg. Once magnesium catches on fire, it burns very hot and is almost impossible to put out. So if the flight engineer saw an engine temperature rising for no apparent reason, the crew was to bail out immediately. Boeing engineers calculated it took only 90 seconds for a magnesium fire to burn through the main wing spar.
http://www.allpar.com/history/military/b-29.html

I am not sure how accurate this man's info is! The only "magnesium" parts that I knew anything about were the "dynafocals", which attached the engine to the wing, in the accessory section. The whole purpose of these was that if the engine caught fire, they would burn into and the engine would fall off the wing! I never heard of one doing that, but did see one land one time in Japan with the #3 engine "drooping" about 20 degrees because the top two mounts had burned into, but it did not fall off the wing.
One thing of note though, if you will look at any of the pictures from that time frame, you will see, waiting on takeoff, long lines of B-29's. The 29, as long as cowl flaps were fully open, did not have a heat problem, the problem came when you closed the cowl flaps to 10 degree settings for takeoff! The reason for that was the vibration of the elevator above 90 knots IAS. Engines 1 and 4 cowl flaps did not effect the elevators like 2 and 3, so our procedure was this, as soon as we approached VR speed on takeoff, usually around 105 to 115 knots IAS, depending on the load, #2 and #3 were placed in trail by the engineer, but 1 and 4 were left at 10 degrees. As soon as we broke ground, if I remember correctly, #1 and 4 were also placed in trail, for accretion purposes as those big old cowl flaps would hinder the acceleration of the aircraft to V4 then to VX then to VY, again depending on load out,, as these speeds varied with load out. Then the engineer would adjust cowl flap settings to what ever opening for cooling purposes, but 2 and 3 were never open more than 10 degrees at any time because of the effect they had on the elevators.
I was never "trained" to bail if we had an engine fire, which we did on serveral occasions during 924 hours in the beast, but always the on board fire protection system would put them out, but we always had to shut down the engine. That was first order of business in the event of a fire!
Not real sure on this, but I believe the R-3350 "compound" engines were re-designed after the A and B models of the 29. The "C" model, which I was envoloved in, had the same engine as the Lockheed 1049G super "connie", and also the first of the Boeing model 377's had the same engine, but later were changed to the R-4360 engine.

But the 1049G always had the R-3350, as far as I know and there may have been some problems with the engine, when you look at the DOT accident reports on this aircraft, I could only fine 2 which crashed due to engine fire.
Maybe this is another case of "reputation" giving the aircraft a bad name through inaccurate information!