The nacelles didn't just droop. Shaw talks about a fix he is working on. I think the fabricators made the mistake of assuming the nacelles and secondary hulls were cylinders. If that was the case, everything would line up well.
My dad shaved the back of the neck pylon. That lined up the saucer with the nacelles, but the secondary hull pointed down and to the front. I liked that, in that the nav dish could 'scan' below--look-down shoot-down radar style.
Now in case anyone else wants to do a model, here is a suggestion. Break the model up into more pieces.
Now the assemblies consist of trying to join three tubes with two struts--and to me that is a mistake. Not just droop, but toe-in, toe-out issues can be expected.
An idea I had would be to make a triangular one piece bracket.
Now imagine That there is a perfect Enterprise model, and that a laser were to cut it (top to bottom--straight down) in two places--right in front of of where the nacelle support pylons join the nacelles to the secondary hull--and another similar cut just behind.
This would leave a triangular bracket not unlike what I have seen on some engines.
Now imagine if a machine tool were to fabricate this, or you had a one piece mold.
The result would be that the join line at the base of the nacelle supports and where they join the truncated nacelle segments up top would now be parts of the model detail itself. No possibility of droop or mis-alignment.
Then you attach the forward and aft nacelle bits to the each top of the bracket FLAT-to-FLAT.
Same with the secondary hull front and back.
The triangular bracket might even have threads where the parts may screw in.
No more droop.