Something about this seems wrong to me.
I am making some changes to a Base Mod by way of an ancillary mod. I open up the GECK and check the Fallout esm the Base Mod esp and the Ancillary Mod esp, I set the Ancillary to Active. The Base mod adds a dozen items to the game, the Ancillary mod makes minor changes to 2 of these items and adds 3 more. I then hand place all 15 items into the gameworld; save changes and close GECK. Now when I fire up Fallout with both mods checked I expect to see all 15 items, but instead I find only 5.

My question is; how do I pull assets from another mod without actually making changes to them?

You cannot mod an ESP, plain and simple.

You either need to convert the master mod into an ESM, pull the master mods objects into your own ESP, or just edit the master mod as is.

Thanks WillieSea, you have just answered several weeks of frustration in 5 words.

The Base mod was still undergoing tweaks and upgrades so I was trying to avoid conflict. I guess that's why all the big team built mods are esms.

As far as I know you actually can modify another esp, the problem is only that the GECK doesn't allow to set esp's as master files. To work around this:

1. Set the esm flag in Fo3Edit for the mod you want to modify by another esp.
2. Load the modifying mod as active file in the GECK, with the modified esp also checked.
3. Remove the esm flag you set in 1.