Hi folks!
I have the same problem since I changed to FS2004. Solving is very simple

Since our 747 has the same flight dynamics like the default 747-400, if you copy the default 747-400's AIR-file over our 747 AIR file, than it will solve the problem. So:
copy ..FS9\Aircraft\b747-400\boeing747-400.air > ..\ehm_744v2\Boeing747-400-MR-MKIII.air
I am sorry that I reported this only now, but I myself discovered the solution only yesterday. I thought that I must edit the CFG file but that did not help really. I worked on it since weeks, but it did not worked quite well. The secret is inside the AIR file

I will analize airplanes one by one and every dynamics bug will be removed. I will add my own additional fix to this plane as well.