What is the main problem here? Not able to identify what to pull from the source or incrementally loading from source or both? 

If you can identify the records that have changed and just need a way to incrementally load them from staging to fact, then just add a row number when exporting from source to staging and load the data incrementally from there? You can also export the source data across multiple files or export to one big file and do another process that partitions that one file into multiple files. Then load from source to staging incrementally as opposed to a full load.

Plenty of ways I think.