While it's easy to replace a light or faucet at a later date, you should have your contractor do the larger tasks at the same time. If you plan to replace the tub and install tile floor, it's best to do that all at once. You may save on labor charges if they can do a few tasks in one day instead of doing these tasks on separate days a few months apart.
The angles where any two planes meet in a wet area, such as the shower, tub, and countertop need to be filled with a flexible material to absorb movement and seal up this section to keep it watertight. This is usually done with some form of caulk 6, either latex or silicone. A tube of caulk 6 costs around $20 and this is usually installed with the tile, shower, or counter with the cost included in the tiling.
As a contractor I can tell you that most reputable contractors probably don't need your job, and if you make things too complicated or troublesome, they will move on to other jobs that don't throw up red flags. Much of what you ask for here is reasonable, but bringing a second contract into the equation can set of some alarms that you may be a difficult customer to work with or even a litigiously minded person who is likely to try and bring a lawsuit whether deserved or not. Anything you want covered should be in the original contract.
Bathroom remodels provide 60 to 70 percent resale returns as a home improvement project. However, this project isn’t cheap. It is essential to plan your remodeling ideas ahead of time. Then, hire a remodeling contractor for the job. Ask questions, set realistic expectations, get accurate cost estimates and budgeting from the start. Also spend time learning how to work with a bathroom contractor.