autumn colours in late September

We MAY be having a very quick trip to Japan in late September for a family function, flying in and out of Narita. We could have a 2 night "window", and will probably have a JR Pass(will be used for N'Ex x 2, and Tokyo-Sendai return...just about worth it)The link on this guide says Alpine route is good in late September (we can't get to Hokkaido): would Matsumoto/Nagano be OK for autumn colours at that time? The Alpine route itself would be too hard for us: we need to be covered by the JR Pass, and will be very time short...we are thinking of a day trip to Nikko, and a long day trip/maybe overnight to Matsumoto. Any advice will be much appreciated..thanks.

You would have to go into the very high elevations of the Japan Alps or other mountains of the norther Kanto or Tohoku region. There might be some colors in the highest areas of the Alpine Route, as you can see in the following blog entry of October 3, 2008:
http://www.japan-guide.com/blog/scott/081003.html

would Matsumoto/Nagano be OK for autumn colours at that time?

No, the city centers do not see autumn colors until much later.

The highest elevations of Nikko might have some coloring, too.

But generally speaking, it is difficult without going to Hokkaido.

Thanks yet again Uji..we may now try to look at possibly Hokkaido.....