It has not caused an issue because I value the learning I had to do to complete the above mentioned items.

Do I have to fill out a separate Federal 4562 for each item and check it off as bonus depreciation, or can I bulk the items together - either all of them total, or the 15s together and the 5s together?

Real estate investor, if you did a cost segregation, amortization, depreciation, 1 time expenses, 1 time closing cost Fee's and this can differ from residential financing compared to 5+ financing.  1 time expenses on properties can be new roof, appliances, A/C and bigger ticket items. 

I have a list of items my PM is recommending to meet the section 8 standards, I want to make sure all of them are necessary.

No bread and butter items purchased only business costs to make money.  

See notes on Rehab Cost Estimates for why this is too low... should be at least 5% + amortizing the cost of any major capital items coming up in the next 5 years. 

@David Traeger I know the Milwaukee market well and have a couple of quick hitting items I can pass along to give you and overview.

they are a way to ensure certain items are completed timely. 

"capital" not "operating" so they don't belong on any metrics that call for operating items (i.e.

"Quite a bit of work" can mean considerable renovation budgets, plus potentially large, expensive, unexpected items that come up in the construction process.Half of a duplex is also an odd situation, but that may be more Canadian than US real estate.It's really a matter of risk vs potential reward.