Andy,
no worries. It looks like it's just down standing flange that gets dollies and trimmed after the trunk filler panel gets installed.
If it fits well everywhere else, secure with screws, then remove the rest of your remaining q-panel. Before you remove the q-panel, make sue to measure the window opening.
Test fit the new q panel mating to the wheelhouse and b-post (door latch) and rocker.
Don't forget to check your fit with the trunk filler panel secured in.
Once you do it on one side, it will go twice as quick.
Best,
dan