I still do not understand...do you feel the aircraft too heavy with the current flight dynamics? Is that the problem?
I think it is usual that on transcontinental flights it is absolutely full. It means there are lots of passengers and full of fuel. In this situation every aircraft is a little bit lazy and SID manouvers are a bit difficult. But when you land it after 10-12 hours, with almost empty tanks, I think it is quite handy. I think the only problem is the speed. As the 747 cannot go below 160 kts it is much harder to keep on the glideslope than a 737. Try to make an approach at 180 kts with the 737, and touchdown around 160-170 kts. I am sure it will be as much difficult as with a normal 747.
If you use it on shorter routes, than try to decrease the fuel load. Average fuel usage is about 3000 gals/hour for the 747, so you can calculate the needed fuel for a desired route. Also you can decrease the number of pax inside the "load" sections of the CFG file.
