2 Week Trip Plan

What I have outlined. Regarding my 3 nights in Kanazawa I'm open to alternative cities/town since it will be over a weekend. Considering Nagano or Matsumoto as alternatives but I have been those 2 before.

Nights 1 & 2 - Tokyo arrival/rest/cleaning

-Take the Shinkansen to Nagoya-

Night 3-7 In Nagoya.
I would like to day trip to Narai and another day trip to(maybe) Takayama. I have been to Hida-Furukawa before so is that repetitive?

-Take the Shirasagi from Nagoya to Kanazawa.-

Nights 8-10 in Kanazawa.
This will be over a weekend so I'm worried about huge crowds there?

-Take Shinkansen from Kanazawa to Tokyo-

Nights 11-14 in Tokyo.

I will have a full JR Pass, taking place in May after Golden Week.

It's all up to what you want of course, but if you've already seen Matsumoto & Nagano before, why go again? There are other places there, but it looks like you didn't consider going in the other direction - Fukui has a number of great places as well. The Tojinbo Cliffs are really nice and one of Japan's most beautiful rugged coastlines, plus there is the Dinosaur Museum, which is really impressive, and the Eiheiji Temple.
https://www.japan-guide.com/e/e6600.html
Not to mention the Echizen Great Buddha, one of the most impressive yet empty places you'll see in Japan.
https://youtu.be/xZPF2SYv00I

Takayama has the same vibe as Furukawa, but is crammed with a lot more day tripping tourists. There is more you can see there though, and if you're not going to Shirakawago, there is the Hida Folk village, a nice open air museum. It's also not clear what all the time in Nagoya is for. Every place has something of course, but there are many other sights elsewhere. If you are in the area though, it would be tragic if you missed the Meiji Mura open air museum in Inuyama - it's the finest in the country, easily.
https://youtu.be/ZgYDE7ujk8A

If you travel after Golden Week, the crowds will have subsided.
Also you may have other unstated travel planned that might make up the difference, but if you start using a 7-day JR pass from Day 3, it will expire at the end of Day 9 in Kanazawa, and you'd be losing money on it. You would also lose using a 14-day pass. You should consider other travel or shortening your trip out of Tokyo.

I'm going to buy a one way discounted Shinkansen ticket to Nagoya. I plan a side trip from Nagoya to The Yamazaki Museum and an early dinner in Osaka or Kyoto and go back to Nagoya. Which all fall within the 7 days pass and I will be coming out ahead (last day of pass going to Tokyo)

Since I'll have 2 full days in Kanazawa I can visit something in around Fukui and still have a full day in Kanazawa.

If you want to go to Takayama and Kanazawa, wouldn�ft it make more sense to go Nagoya-Takayama-Kanazawa without back tracking?

Yes, it adds one change of hotel, but also gives you several hours that otherwise would have been spent on transport.

Enjoy your trip to Japan!