Thanks for confirming that Floyd
Thats actually how i first started but i thought it would make everything too high and not work.
Looking at the pics do you think i can fit the p-traps in there? One hole is kinda offset from the other 2
The bulkheads are 1.5''
The inside of the box is 27.25''
We need to stop right here, and go back to the beginning. You are fixing to change the whole drain system for a problem that is simply caused by one of three things: The air vent line too low in the overflow, (the most obvious problem in your original photos,) the outlets to the drain lines are too deep in the sump, > 1", (second most obvious problem) or three, the bulkheads are too large for the flow rate. Generally you do not need 1.5" bulkheads for a flow rate under ~ 2000gph. If the flow rate is too low enough, 1.5" bulkheads will not back up the water level enough in the overflow to start the siphon. Invariably, every time this starting issue comes up, it is one of those three things. Only the later requires modifications to the system, the other two just need corrected.
There are no mysterious issues that need to be chased around in circles, and the top end plumbing configuration has nothing to do with your starting issue. As far as the tees on the top end, they have nothing to do with either the function, or the sealing of the system (if all external.) The tees and caps as simply a service access: Unscrew a cap, run a bottle brush through the drain line from top to bottom, put the cap back on. Pretty simple. With well over 250 of these systems running I have yet to run across a single problem with this system related to the tees and caps, well unless you don't seal the cap properly. Nor I have had and problem with the height relationship between the siphon and the dry emergency. The raising of the open channel inlet by 1/2" is a quick fix for the over-sized bulkhead issue, if that is the issue involved. People just don't think about this sort of thing, so attribute such in ways that seem to make sense, making things more complicated than they need to be.
This system works as designed. Your implementation is "as designed" save for the bulkheads being under the tees, rather than before the tee. Floyd's system is not a BA as designed, it is heavily modified, and it will not work the same as a BA, therefore the setup needs to be different, to achieve the proper function. The 'p' trap open channel cannot be at the same level as the siphon, other wise the open channel would trip to siphon during start up, and the siphon would not start—which is one of the causes for your issue. This system worked on the original design, and every other properly implemented system, with the elbows at the same level.
You don't need to change the configuration of the drain top ends. But looking it at, I think the top ends need to come up higher in the overflow. You have a pretty long waterfall into the overflow. You need to sort out the errors made, if any, and get it adjusted properly.
Your issue with the return section running dry is because there is not enough water in the system. Water in will always equal water out. If water goes up to the tank, and does not drain down and fill the return section again (after going through other sections) where is the water going? If it is not going down the drain, it would be flooding the floor. If you don't have enough water in the system in the first place, the drain system will not start anyway. Therefore you need more water in the system.
Those are the problems with this system.