To follow up:
1st off, my rear spar wasn't straight which caused my misalignment issues. Not sure why I dind't think to check that in the first place! A straightedge held from top to bottom had the bottom recessed about 1/8". I thought, let me add a tiny bit of bend back to the spar/doubler to get things into alignment. That worked, but of course those spars with the bent flanges don't like bending. The flange puckered out about 1/16" similar to when you flute a rib.
So, I spoke to Kevin @Van's. (He's always great to talk to). That spar doesn't have a need to carry much foreward/aft strength, so it's not an issue if that puckered. The design load is side to side on that and the front spar/plate is the strong piece for the forward/aft movement. He said from there, any small gap left next to the W-712D elevator stop can be clamped out and drilled. Some pre-load isn't an issue. He also said the rod end bearings can adjust out any slight alignment issues so not to worry that much about it, just make sure the whole thing is plumb and square to the fuselage.
Lessons: when building the vertial stabilizer, besides the obvious as others have said, don't trim the 5/8" off the forward spar until you're ready to bolt this thing together. Also, make sure your rear spar and doubler are straight before riveting those together. It'll make life less interesting when you get to the assembly stage.
My 2 cents, YMMV as they say.