I Am in a Off-the-Grid Location 70 Miles North of Fairbanks.

I am in a off-the-grid location 70 miles north of Fairbanks. This camp is fairly new and they are expanding their power needs in the shop area which consists of 3 conexes. So we have set up a Cat genset for supply; 81 KVA - 65 KW .8 cos, 3 phase 12 wire,wye conf., connections-series,. The neutral and ground from the generator are bonded together in the panel on the generator. In that panel is a 100 amp 3 pole breaker from which I have taken leads to the power shed to feed two fused disconnects. From that point we have (2) transformers.....#1 is a 45 KVA to feed conex 1 & 2 and # 2 transformer is a 30 KVA to feed conex 3. Now to the problem; #1 transformer has a factory bond from the XO terminal to the frame, and transformer #2 does not. Now if I understand the code, an outdoor generator needs to be grounded at the generator, but also the ground and neutral can only be bonded at one location. Do you see my dilemma ?
Thanks, Bill