new frame and skid plate issue

I took my stock skid off a long time ago. Never got around to putting it back on, did the frame recall and painted up the skid so it all looks pretty when I decide to put it back on. Looks like it doesn't like up quite right and where it does look like it will the bolt holes are a different size than what came off, there is also a significant gap.

I'll try to get some pictures up, but really what I'm asking is anyone have any issues after a new frame with things not lining up?

Or even if I went aftermarket it's all based on stock hardware locations, right?

It just looks goofy and not protected underneath anymore....ugh