Yes, those inner cowl panels don't quite match the replacement floors or the inner-to-outer cowl panels, but can be modified to fit. It'll take some hammering and probably a little heat to get the job done. Click on this
link and scroll left to see the photos of the work I did in that area.
I bought the shorter inner cowl panels as well, which fit better, but I decided not to use them (didn't want an additional weld joint), and made the ones I got from Jim Carter work.
If you have more questions (and I'm sure you will) feel free to ask. You might also post some pics of where you are, so we can get a better handle and possibly help out more.
The holes on the rocker panel are only needed on the driver's side, although both of the replacement rockers I got had holes in front. Don't worry about the lack of them on the passenger side cowl inner-to-outer panel.
Here's another post of mine with pics on the subject.
LinkHere's the thread where I asked the collective of knowledgeable guys basically the same question you did.
LinkHere is the start of progress posts I made in the "What did you get done on your bolt today" on that area. Scroll forward in that thread there for more info. I should really put those in the Project Journal forum so they're not so hard to track down.