Using 2 rail passes with gap in between?

Hi,

I've traveled to Japan on many occasions and have enjoyed the JR Rail pass immensely.
My next trip I'm taking is a little different.
I'm going to be spending 5 days traveling in the Tokyo, Yokohama area, then I'm joining a tour group which is taking care of all the travel expenses. Then I'll be on my own again starting in Kyoto, traveling to Kamifukawa, and ending in Nagoya.

So my question is this....I know I can get a Tokyo specific rail pass (and same money), can I also get a regular rail pass to cover the second apart of my trip?

Essentially, can I buy 2 rail passes, a week long pass for Tokyo, and a week long pass for the end of my trip?
And, if I can...do I get them both exchanged at the same time? Of, if I do that would that mean they both cover only the first week of my trip.
Please help.
~Rylin