We use Autotrack for sweep paths through projects but I have not used the vertical path routines. I have only had to estimate vertical clearance for a couple of jobs and I have done it with profiles. I would really try to get one of the software packages to help with this but in the event of that not happening...
"I'm not sure how to model the gooseneck pivot and the other 3-5 axles or even if it's necessary"
I would think the model would need to be pretty specific for the tractor trailer combos used. Different 5th wheels, different 5th wheel locations and heights, tractor trailer sizes and king pin locations should have an affect on this. A low boy will probably have a fully oscillationg 5th wheel to allow for more side to side deflection as well. I think these mount a bit higher. You should be able to measure the deflection on a fith wheel without a trailer attached. It may take a few people and be quite greasy but you should be able to see how the 5th wheel pins in all directions. Max deflection between tractor and trailer should come to light when you draft this up. You may see the front of trailer hit the tractor frame or the top/rear of the tractor frame hit the bottom of the trailer but the limits should be seen.
I would think the number of trailer axles is important to model since you could have a situation where one axle may support the entire trailer and the other two would be in the air. You would also want to monitor the rear trailer overhang and make sure that this does not hit the ground.
C3D 2012, RD 2012
Win 7 64, Core i7,
6 GB RAM, Quadro FX 1700