My advice would be to use universal patcher, as it does not require an XDF, and also is capable of seg swaps, and also fixes checksums everytime you save a file.
To seg swap, you have to have a bin that has the same os as your original file with the seg you want swapped. So you need to look and see what manual bins are available. You may need to change is. Things to look for if changing os, drive by wire vs drive by cable, 1meg p59 vs 512k p01. Make sure the 5.3 file you swap trans section to, matches your original file for these things.

Bin files can be found here
http://www.gearhead-efi.com/Fuel-Inj...BDII-Bin-Files

Universal Patcher can be found here
http://www.gearhead-efi.com/Fuel-Inj...versal-Patcher

Hope that helps