Due to the way the B-29 was loaded in real life, you can OVER LOAD it past max take-off in this game by mix-matching too much fuel and too much bombs. 40x500 is the max load of bombs. That means you CANNOT take the max fuel. I mean, realistically it's possible in this game, but you're lifting off beyond max takeoff weight limits and the airframe wasn't designed for that. If you want that many bombs, fly at reduced power once you're up to save fuel (that's how they did it in the war -- couldn't fly to Japan and back unless you cruised the entire way there and back).
Those max bomb loads were never dropped from extreme alts. They were carpet bombed from much lower alts. They looked at the mission profile and found out how much fuel they'd need to get to target alt (which wasn't very high), to cruise to target and back, and then how much free space was left. They filled that space with bombs. Some of these missions came in between 5k and 10k alt, though in the dark of night for protection.
For the missions that went up into the rare air, they flew with much smaller bombloads. Often only 5000 lbs or so on the longest and highest missions. The absolute maximum was around 125,000 lbs for MTO weight. Some sources say this stretches up to 130,000-35,000 ish, but 125,000 seems to be a better mean weight for MTO.
In AH when you take 40x500lb bombs and 100% fuel, you are just shy of 145,000 lbs. WAY overloaded. When you take 40x500lb and 75% you're still way overloaded at just shy of 135,000 lbs. At 50% fuel you finally get under the MTO by getting your weight down to about just shy of 125,000 lbs. And that was WITH a 10,000 foot smooth runway to assist in prolonged takeoffs.
Moral of the story is: Don't take 40 eggs if you want a long sortie. Taking extra fuel doesn't solve the problem, because your time to climb is in the toilet now, and your acceleration time if you ever level is utter crap too. You screw up your entire flight and make it 20x worse on yourself. Come in lower, or take less bombs, but either way fly LIGHTER. Take the 20x500lb load if you want full fuel. 20x500lb and 75% is just shy of the 125,000lb MTO, and 20x500lb and 100% is just shy of the hypothetical 135,000 lbs MTO.
40x500lbs was never meant to be anything other than a low and fast drop. You want to take it up to 35k, you're going to suffer the pains of doing so. I.E. crap takeoffs, crap climbs, crap accelerations, and crap turnaround times on repeat drops.