Northern Iran, what are the most beautiful place (not tourist) not to miss?
There are still pretty few touristy places in Iran. Highlights of the north for me would be (west to east)
- Armenian Churches at DzorDzor, Chaldran and in the Aras Valley

- Old Bazaar of Tabriz

- Mausoleum of Hulagu Khan in Soltaniyeh

- Old Bazaar of Qazvin

- Road from Andabil (not Ardabil) to Asalem

- Backroads of Mazandaran which go through beautiful Caspian forest

-Lar Plains and Mt Damavand

-Shrine of Khaled Nabi in Golestan
I guess you will cross the border to Ashgabat, so I won't go further east, but Semnan, Neyshapur, Mashhad, Torbat-e Jam and Taybad are all fantastic old cities on the Tabriz - Herat caravan route.
Turkmenistan visa I will have to go through, you can join Ashgabat. The gas crater and Merv.
how many day you think for this , because the visa for travel visa is short.
You will only get (at best) a 5 day transit visa unless you pay for a tour. It is possible to see Asghabat, Darvaza, then turn back and go through Mary (for Merv) and Turkmenabat to Uzbekistan, but you will be breaking the rules of your transit visa and could get into trouble (I speak from experience). But Merv is the most interesting historical site in the country, though Konye Urgench is also great.
What border is open for going to uzbeckistan to Dushanbe?
The most convenient is at Sariosiyo / Tursonzade on the M41 between Termiz and Dushanbe. I have also crossed the border at Oybek (south of Tashkent) and Konibodom (south of Kokand) which both lead t Khujand rather than Dushanbe (Khujand is a more interesting place than Dushanbe BTW)
In China what agency you know ? because my agency (desert_rose , she is too expensive.) to go to Torugart border (near Naryn in Kirgyzstan and Aksu in china)) and Bulgan or Togrog border (near Urumqi in China)) and after in Mongolia.
Can't help you here I am afraid
Already went to the Pamir in 2013,but i don't know if in June in Kirguizstan the tracks are not so muddy?
You should be fine.