Was just having a look at Quest for Performance, from the NASA history office, and it says that the B-29 has a service ceiling of 31,850 feet and a maximum speed of 357mph. Is that the loaded weight, or is our B-29 one hell of a super-modified Superfortress?

The B-29C/RB was the lightest 29 and could exceed the 31K listed service ceiling quite easily. I have been to 36,500 a couple of times, dodging weather. The aircraft we have in the game is a good aircraft, but there are some things which one must remember when flying our 29.
#1- takeoff with flaps up and auto-takeoff function engaged until you get proficient in flying the aircraft. Make no turns until at least 1,000 feet AGL, and make all turns standard rate turns. (3 degrees per second)
#2- When descending for landing, stay under 325MPH IAS, as parts begin to leave the aircraft above that figure.
#3- When climbing in auto pilot, 50% fuel and 40 500lbers, use dot speed 175, as it will get you to altitude quicker.
#4- If your start a turn when in auto climb, the aircraft nose will drop considerably when you start the turn, so use a good bit of up elevator to maintain your climb rate.
#5- The bomb bay doors will assist you a little in descending by being open, but best to push nose down slightly below horizon, engage shft + X, then adjust speed with throttles.
#6- After dropping bombs, nose will balloon up quickly, be prepared for that, after disengaging auto pilot.
#7- I use 150MPH downwind in pattern, 125MPH on base, 115 on final, with bleeding speed to 100 over the fence and I plan on touch down in first 25% of runway. (Just remember, there are 2 things you can never USE when in the pattern with any aircraft, especially a heavy aircraft like the 29 and that is altitude above you and runway behind you, so plan ahead at all times).