The PiScan software is strictly for the Raspberry Pi. The advantage is that you can do all the scanning without having to hook it up to a computer. There is software that will run on a PC. If you load CHDK on the camera, which you need for PiScan anyway, you can control it using PtpCamGui
http://chdk.wikia.com/wiki/PtpCamGui. Twocamcontrol adds the ability to control 2 cameras at the same time
https://github.com/nod5/TwoCamControl. I had some problems getting everything working for that, and I was having the gutter problem.
The gutter problem isn't the gutter itself. The problem is that the edge of the platen on one page covers the ends of the lines on the other page, so you wind up having to do some heavy editing to correct almost all the lines that go down into the gutter.
If you look you can see that the edge of the plastic I am using for the platen is thicker than the distance from the text to the gutter. So the scan misses a character at the gutter end of each line. By using only one camera, and one sheet of plastic, the problem isn't there. There may be other ways to take care of the problem. If you can find a thin enough sheet of glass that is very strong (Gorilla Glass?) you might be able to do a 2 camera system that minimizes the problem. I don't know if there is such a thing.
I am using ABBYY FineReader 14 for OCR. With it I don't have to rotate or crop the image, the software does it for me. I do occasionally wind up with an image, fingers and such like, in the middle of the file, but those are easily deleted. There is a free software package, FreeOCR
http://www.paperfile.net/ . This includes the ability to rotate and crop the images in the software. It does require that you process each page separately, and leaves carriage returns at the end of each line. There is a relatively simple process that can use the search and replace function in a word processor to correct that problem.
Creating the images for the scan takes me about twice as long as with a 2 camera system. I have been keeping track of the times for scanning a book lately. The longest scan time that I have is 50 minutes for a 300 page book. It took me 40 minutes to scan a 187 page book. However, this is just the start of the process of creating a digital book. The rest of the process is what takes the longest time. The total time I have spent from start of the scan to a finished ebook, in EPUB format, has ranged from 20 hours to 50 hours. The 50 hour one was a 300 page book with complex formatting, and strange words that had to be individually checked for spelling and format. The 20 hour one was 187 pages, basically written in plain english. The longest time was the time spent editing the book to correct the errors that occur because no OCR software is 100% accurate. It takes a lot of editing to catch most of the mistakes. I did an average on the time required to finish a book. It turned out that I have been finishing books at the rate of 7 pages per hour. That is an average, any given book make take a longer or shorter time, but it should give a good rough estimate for any book.
I think your choice of the Nikon for use in both scanning and for general purpose photography is probably a good one. It might give you better results for the OCR process than the Canons. Maybe it wouldn't keep turning 'rn' into 'm'.
Bill