This is going to be a long process, isn't it?
Sad to say, yes it will likely be.
I had someone back into my parked car and it took over 7 months for the paperwork to be completed and damaged to be fixed. All that took was a bumper replaced. You have a lot more damage involved.
Has your vehicle been checked thoroughly to make sure the frame wasn't bent? Your accident was serious enough sounding that I cannot believe the vehicle wasn't consigned as being totalled.
I don't have much faith that it will drive straight and true after being rammed in the side like that. Personally, I would not consider that type of collision as safely repairable. Is there any possibility of a second opinion from Honda or the insurance company to see if it can be totalled and you receive monies or a replacement vehicle?
Think of it this way. By law, you are required to disclose that this vehicle has been in a major accident when you go to sell it. The blue book value & desirability has automatically dropped drastically because of this.
The other major issue -- now that the vehicle has been sorely stressed like this, could you trust its integrity in a second major accident if one happened? I don't know how liable the repair shop and your insurance company if it was determined that the condition of the vehicle increased damage in an accident or not. Would you risk your family and your life in the belief that everything was fixed as good as new?
The whole issue with your seatbelts, imo, doesn't bode well, especially their response when you came back a 2nd time. They might know what should be replaced, but I bet they'll try to nickle and dime you the entire time. This is not confidence building in the least.
I had a friend who's car (a Neon) was stolen while we were in El Paso, TX 11 years ago. It was used in drug deals and there was a police chase where it was driven high speeds off road. It hit a large rock and landed on its side. The body shop repaired it, but she swore it never drove right after that. No matter how the alignment was fixed, it kind of went sideways down the road. She ended up trading it in to the dealership for a newer car. They dropped the price $3500 below its blue book value and she took it because she couldn't sell it privately.
good luck