Take all closing costs except currently deductible carrying costs like interest, taxes and insurance.Set it up for amortization over the length of the new loan, starting on refi date.There is no land allocation involved,Whatever is left of the old loan costs should be deducted now.

One thinks that General Partners can't take depreciation on their carried interest (until all Limited Partner capital accounts go negative), only on actual cash contributed and the other thinks that allocating depreciation based on overall sponsor ownership (vs cash contributed) is correct.

Again allocate part of the price to that.  

That along with various fines that existed before I took over ate through a lot of my capital that I had allocated.

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.