For brevity's sake, I understand the merit of seller's not paying professionals to negotiate against them and I am a proponent of brokers having greater flexibility and influence on compensation allocated, as it provides all parties greater chance of compromise. 

As for the cash you put into the LLC you could allocate it different ways, as a capital contribution or as a loan to the LLC.

Allocating 10% each for vacancy, maintenance, Cap-X, and management you should set aside a minimum of $250/month. 

Would it be fair to allocate these items as capital expenditures?  

The principal is being pre-paid in comparison to how the loan is amortized, which is the schedule of principal and interest payments and allocations of the same.

I've allocated 5% for vacancies since they've all been in areas that will not have extended vacancies. 

The basis of the original property is divided appropriately and depreciation is allocated prorata so that your adjusted cost basis is accurate and you then have only the allocated gain from that one unit to content with.  

Using the example above, the cost segregation allocations apply to “net tax basis” of $1,200,000 ($700,000 carryover + $500,000 excess basis).

I incorporated the cost to pump the sewer into the maintenance allocation since it is a biannual expense. 

Any new money added to the basis to complete the purchase, that is allocated to the replacement property improvements, is depreciated on a separate 27.5 year depreciation schedule.So, you see that you only get ten years of depreciation on the first $250K of the replacement property basis, not the 27.5 years that might be allowed over the class life of the property if it were purchased outright rather than acquired in an exchange.HTH