Oh sure, go ahead and confuse me with floor pan talk
Assuming you havn't changed any of your 'settings' on the door hinge (washer spacings, etc...) and the fiberglass hasn't magically moved (I know a lot of people say it's a living creature, but after 4 fiberglass cars and extreme temp changes, -50*c to +30*c, I've never seen it happen), I'd look at 2 things from my experiences
1 - From the last time the doors worked properly have you done anything that would "touch" the spyder section (e.g., when you closed up the rear firewall gap, did the doors work properly after that or is this the first time you've put them on since). I've found that it is very sensitive to small changes - for example, I tried a small piece of bulb seal on the rear firewall. Even though the spyder was bolted down, the bulb seal twisted the top of it juuuust slightly such that my rear clip didn't sit right anymore (couldn't latch my quick release pins) and my door didn't latch properly anymore. So from that I've been leery to seal up the rear firewall and instead make certain I have a slight gap to ensure the spyder isn't sitting on anything.
2 - The lower door hinge is incredibly sensitive to how you tighten it. For example, on the forward-most nuts, if I turn them an extra 1/4 turn I can go from the bottom of the door and the sides being perfectly even to the the bottom kicked out 1/8'' and the sides twisted inwards. Just from a slight 1/4 turn. Alternatively on the rear-most nuts if you tighten them more than hand tight you can twist the door unintentionally (I end up hand-tightening them, then back up with a nylock down the road). SO basically I'm just trying to see if you're tightening down the front hinge the same as before, because I've found an extra 1/8 of a turn of a nut can have a HUGE impact on if the door can latch and how it sits.
Failing that, I'm not certain - that's about all I ran into that caused the door to twist and not align/latch properly. I suppose worst case is you just undo your striker and move it around a bit in the slot until it latches fully again.