There are two 57 mm systems. You have the “banana” system. The silencer looks like the stainless version to me, but it’s hard to tell from the photo (at least for me). Weigh it and I can compare to my SS and Ti versions.
The air runners appear to have been replaced with CF aftermarket versions, hence the missing overflow tank. The air box appears to be OEM though, so finding original air runners should be easy.
No idea on the drilled and tapped frame. Personally, I’d have them welded up and then repaint the frame.
Best of luck with the project!
1998 SS FE #194
2005 749R #362
2006 999 S