Provided that Jake has actually implemented your extended organ definition to be compatible with the original one, then you should just need to use just need to use 'Registration | Import combination set' with the new organ loaded to import any desired combination set from the original.
Since they're different organs (IDs), you will always be shown the following prompt when doing so, but it's just a warning, and you can safely just click 'yes' if they are actually compatible:
This combination set was saved with a different organ. Loading a combination set from an incompatible organ will give unexpected registrations or results.
Are you sure you want to import and load it for this organ?
Select 'No' unless the sample set producer has specifically stated that combination sets from both organs are designed to be fully compatible with each other.
Check with Jake if in doubt about whether they're compatible, but if he just adding some extensions to the original organ's definition, then I would imagine that he would have made them compatible (i.e. that he would have retained the same switch and combination IDs for the existing stops in the organ definition).