I just read all of what was posted, that took a minute. But very informative bravo gents and ladies?
Coming into this 'fresh' it appears that there are only a few options each worst than the last.
A) Mismatch top feed (3 pin) TGVs with the plastic manifold. The computer might be happy, nothing lines up exactly right, but hey you can use top feed injectors. This requires filling the center holes with weld or epoxy then drilling and tapping new faster holes.
B) Top feed (3 pin) TGVs and swap you manifold while your at it. Not the craziest option, but you will get nickel and dimmed to who knows what final amount. Its only money right...
C) Run the (OME) side feeds, remove the flaps and leave the link bar to keep the ECU happy. You will need more expensive side feed injectors, but again its only money... FUK!!!
C part II) Side feed (3 pin) housings but use side feed conversion adapters, however they leak sometimes. This is an option for top-feed injectors but not a great one.
D) If you fear the man, leave the TGVs as is and run side feeds. Save yourself this one particular headache.
E) Try to run the (5 pin) TGVs try to engineer a some kind of electrical trickery (Arduino some other custom circuit maybe??) to convert the signals to the appropriate values given the position of the flaps.
F) Last and most ridiculous option. Have someone model the TGV housings with the correct bolt pattern for the plastic manifold that also accepts the dual connector config. This has to also consider the bolt spacing for the top feed fuel rails. I have to look at the pics again to clarify this point, but this seems like a dead end anyways. Even if you can 3d print some prototypes machining the real deal is another thing altogether.
I am trying to get my project going, yet again... I was all excited to get my Ebay top feed TGVs (which we mislabeled so FML), its a 5 pin. But this seems to be a waste unless I go the manifold route and get the right housings to start.