My quick answers:
1. What shots do you recommend for Bali? I already got my Hep A/Hep B. My reading tells me that I also need typhoid.
None.
2. Re: mosquitos day and night
Do I really need to cover up completely and put DEET on my hands and face whenever I go outside?
Use repellent when you are out and notice mosquitoes. Keep them away when you are sleeping by using nets or air-con or coils or Hit.
3. My research tells me that malaria pills aren't necessary or useful. Opinions?
Correct.
4. My biggest disappointment is not being able to swim in fresh water--is there any way to safeguard against parasites?
Swimming pools are perfectly safe as long as the chlorine doesn't get you. Lakes are OK I think. Rivers probably OK.
Take a look at this recent thread:
https://balipod.com/forum/threads/health-questions.7194/