Something this detailed and complex sounds more like an op than a flashpoint.
Flashpoints take less than an hour max if the group is badly undergeared, or somebody runs too far ahead because they assume "everybody knows" the path to take to skip all the trash. (I think 75% of FP wipes are from not quite skipping trash)
A well geared group can clear several of them in 15 to 20 minutes.
Good point, flashpoints are rather short, and this is quite complex. A simple adjustment would be to have 2 people of the operation group go down one of the paths, instead of 1, and make the enemies harder, accordingly