See if they can give you an itemized scope of work.

Go over the bid line by line and decide what repairs you need to move forward with and what you don't need and remove the unwanted items from the bid. 

The true value of RE is in what those two items represent in the form of future cash flow and property value. 

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?

You’d be wise to look at migration rates, diversity/resiliency of the economy.

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.