It's a little hard to tell from your post, but I will give it a stab.
If the dist. boxes are downstream from the main service disconnect, there is no limitation on distance that distribution box can be, or needs to be. If the new distribution box is the actual service disconnect, then it needs to be at a location as close to where the utility power enter the building.
The idea is to keep the unfused leads to a minimum. If there are fuses or breakers ahead of these leads, then there is overload and short circuit protection for them, so there is no length maximum.
The main disconnect must shut off all power. If the main disconnect just shuts off the 6 HVAC units, but not the feed thru part, then you have a code violation, unless the next box is right next to the main disconnect. The violations would be, disconnects not grouped, unprotected conductors, and could be # of disconnects (which can only be 6 maximum), among others.
Have the 400amp disconnect everything, and put you dist. panels wherever (working clearences code acceptable) you want to.