<<Disclaimer: Verify this information before applying it to your situation.>>

Thanks to all those of you who kindly responded.

I summaries as follows:

Duchan Gan Shmuel (the biggest store with some very good products).
Contact: Mirta Oren  06-6320892 - 06-6320071/8

Jaffa: A bakery that supply most of the GF breads and cookies to all others
stores.
In  Shderot Jerusalem  (Not far from Noga theater)

Nazareth:
HaTrufa HaTiv'it
6 Paulos St. (opp. "Delek" station) 06-6574126

Haifa:
Super Keren HaYesod,
25 Keren HaYesod, Rommema HaYeshana (just behind the basketball  hall)
Contact: Avi
04-8342442 - 04-8342216

Jerusalem:
Super Kolbotek
3 Kanfei Nesharim, Merkaz Shatner, Givat Shaul
Contact: Arieh
02-6524436/7

Beer Sheva:
Super Maimon No. 1 Shuk Ironi, 07-6274179

Rishon:
Teva Kol, 88 Herzel, Contact: Avi
03-9699239

Hope this helps to others in the list.
Amnon