Or simply how much they want to pay to build it. Working 7 days a week, or multiple shifts is expensive. Add in that you are working with artists and not just raw construction.. it gets even more difficult.
IMO... the delay is simply how long its going to take for the project to complete. We know the plans changed to bring the coaster back into play.. so maybe the pre-construction work wasn't as complete as the rest of the project.. as well as the lead time necessary to get the train systems constructed from the vendor, etc. It may have simply started 'late' compared to the rest of the project.
To your first paragraph, this is very much true. A small example would be when they solicited bids for the refurb of the Joe Potter Ferry Boat last year. They asked for an "Add Alternate" price to complete the work in a specified shorter time frame.
Getting something done faster costs more. Running 2 or 3 shifts means many workers are getting double pay, or at least premium pay for working shift-work. If they work weekends or holidays, that's big time pay, and almost guarantees everyone going into overtime.
Disney has to weigh all these options - the intangible ROI of opening the attraction earlier vs paying almost double labor to get it done a few months sooner.
As for the delays, you're right about those too. I was corrected when I assumed the Mine Ride wasn't on the original plan. So, with that said, it was still probably just a rendering. I don't know if they went so far as to submit plans to the Drainage Board that included a coaster, but if they did, I never saw them. The first round of leaked plans showed the MnG's in the middle.
That means they spent all their design time on the MnG scheme. When they switched horses, there was a lot of re-design taking place furiously. They didn't have to go back through the Drainage Board, since they didn't change water management, but they had to produce Site Development plans and get that work going while the area was still within the confines of Phase 1. Meanwhile they produced full working drawings for the ride itself, which would have never been produced if the project was tabled.
While staggered opening of attractions is good from a marketing point of view, the significant delay of the Mine Train opening is almost completely because they were significantly behind the ball on it from the beginning.