Hi, Xin-
Thanks for sharing the ve2a and va2t images---in both cases, the alignment looks good to me, so I expect the overall alignment (which is just the concatenation of those) should be good.
To check the modeling a bit, could you also please share the vstat image, so we can see what your F-stat patterns from modeling look like? We should see places where F-stat is large, which means where the regression model explains a lot of the input well.
-pt