Have you checked for twist in the HS?
I also had a misalignment with the HS rear spar, however, I determined that I had somehow introduced a twist in the HS during assembly. The twist was not obvious and I don't know how it occurred as all holes had aligned perfectly during assembly prior to the rear spar not aligning. Here's a quote from another post I had done on this issue.
"I ended up remeasuring the HS for twist by comparing plumb lines along the end ribs' tooling holes and determined there was a twist of approx. 15/32 of an inch. I have no idea how or why this occurred as all holes during construction lined up. I went on the assumption that I had somehow introduced the twist while riveting the end ribs, as I had taken the structure out of the cradles and laid it flat to rivet those holes. On that assumption, I drilled out the rivets in the end ribs, then cleco'd the rear spar into place with a cleco in every hole. I then re-riveted the end ribs. After doing that the twist was measured at approx. 7/32. I then riveted the rear spar (my original spar) to the ribs, starting inboard and working outboard, alternating between the left side and right side after each rib. After that the twist was down to about 1/8" and the rivets for the skin to spar lined up perfectly. After riveting the skin to the spar the twist is down to about 1/16 - 3/32, which, I assume, is irrelevant."
Hang in there, I know it's frustrating. Let me know if you have questions about my circumstance.
RV 14A Emp. Complete
Fuselage in progress.