FFE is an useful tool when used in the correct circumstances but it is not a 3d work tool.
Changing texture paths is more efficient in FFE than in 3dsmax as it is basically a textual change. RT2 found ways to "fix" some models to allow them to be imported to 3dsmax but for any other major changes nothing replaces actual 3d work to keep models optimized.
Even with the most well performed FFE conversion there is always some kind of overhead or corruption of the model. Although it might not be noticeable in most cases there are always some issues under the "hood".
For something as important as the OP mod actual 3dsmax work is always the best option