Umm, makes me wonder if you got a set of the headers made late on Friday ?
You shouldn't have to fight the install like that, hopefully it'll be because of the jack stands as you mentioned.
If you go underneath and check where the disptick goes, you'll figure it must be locked in place by pressure, probably orings or something similar in shape ?, it seems you just have to line the end of the tube in the hole, and push it down, Lol, we're all used to this procedure ?
I didn't do the install myself, but watched the install, and i also checked how the disptick is positioned in place a couple of days ago when i was doing my oil change. The portion of the dipstick you grab with your finger to check the oil, won't clear the header primaries without a thick washer as well. something to keep in mind in case you get to bolt the items without any other issue.
If you bought them new, perhaps you should consider returning them and getting a new set, i know it sucks to be there, almost at the point you know you can get it to work, only to find it doesn't fit because the item is messed/bended or whatever.
Good luck dude.
Forgot to mention, the passenger side flange in mine, is closer to the floorboard compared to the driver side, not by much, but i noticed that too 2 days ago while changing the oil, there is no way the flange would hit the heat shield for example or anything aorund it, there is enough clearance for that, and the reason i always say this ****ers doesn't hang low compared to to other systems, i can try to take some pics for you tomorrow morning so you can have a better idea. (if it doesn't rain around here
), i can mount her in my dino ramps and snap some pics.