I think you are getting close. If you truly want only 6 fragment transitions, then you are choosing the wrong option "From filtered ion charges and types plus filtered product ions" on the Transition Settings - Library tab. This will give you the union of your 6 transitions and everything else in your heuristic transition filter.
You want to choose either "From filtered ion charges and types" (which will ignore your other filter settings) or "From filtered product ions" which will apply your entire filter and only use library peaks which meet your filter criteria. The MacCoss lab often uses an "ion 3" to "last ion" filter and the "From filtered product ions" option.
It is highly unusual to choose the option you have chosen, and I have considered removing it entirely because of its potential to cause confusion.
I am not clear, however, on how you got to where you have chromatograms extracted from only a subset of the transitions in your Targets list. It seems like maybe you had different targets when you last re-imported your data files.
Anyway, you are close. Try one of the two options I have suggested to prove to yourself that you can get a set of targets with 6 product ion transitions matching your library and properly including neutral loss ions. Then and only then, re-import your data files, and you should be set to do your analysis.
Thanks for the new screenshots. Good luck with your research.