There's not a course out there, that can teach what you to expect as obstacles on most jobs. It all starts with having some type of experience in the trade and knowing and anticipating the obstacles that you will encounter. You can teach anyone what fittings they are looking at on a blueprint, what you can't teach is understanding the structural conditions that you will encounter to install the fittings that are usually isometrically drawn on a plan. Those are the things that will kill you on an estimate. The other big thing is always job-site logistics. Most do not account for getting tools and materials to the area you have to work in. The time spent moving fixtures across a building can be a very daunting and real expense.
The best thing you can do is learn to break large jobs in to small pieces, and do your best to interpret structural conditions, logistics and obstacles. Then do a very in depth post mortem to see where you were on and where you were off, collect and catalog your data, and learn from the mistakes that you will certainly make. It's truly all about the data, and there is not one magic number for items, different companies, and even different employees within those companies, have different production rates.