So allocations and reserves for vacancies, and legal could be vastly different.  3.

The miscellaneous expense is what I am allocating for reserves.

Here is an excerpt from an article on the subject that I believe breaks this down fairly well:Gain, to the extent of the depreciation claimed that exceeds what would have been allowable under straight-line depreciation, will be recaptured as ordinary income, and, thus, taxed at rates as high as 35% in 2003 and later years (ordinary income rates), but the amount of excess depreciation subject to recapture may be less for certain low-income housingGain, to the extent of the depreciation that isn't recaptured as ordinary income, will be taxed at a rate of 25%.The balance of the gain will be taxed at a rate of 15%Example – In January 1986, you paid $1.3 million for an apartment building (not a low-income building), of which $1 million was allocated to the improvements.

If you're holding the property for awhile you should probably allocate some of the income for those items.

My husband and I paid all our debt (mortgage, student loans, credit cards) off as soon as we could so that we had maximum control of our allocation. 

Bottom line, your note won't have much to do with the disposition of assets or equities except that she will have other equities and less liabilities, that may be offset, it could mean that if liabilities were not equal the difference could be made up in the asset allocations....I doubt you'd get that deep in a customary divorce. 

I'm sure money can be made, but I figure why not keep pumping money into index funds and allocate a smaller chunk of my capital into lower cost RE markets? 

The above provisions relating to Landlord's right to terminate the Lease and relating to the allocation of bonus rent are independently negotiated terms of the Lease which constitute a material inducement for the Landlord to enter into the Lease, and are agreed by the parties to be commercially

I currently rent an apartment and I get a lease incentive from my company for about 50% of the rent, but due to the family expansion I will be needing more space soon.For simplicity, if there is 100K that can be allocated for this, what do you think is the best option here:1.

Comingling those can cause nightmares on past depreciation taken, I suggest you decide what the funds are to be used for, allocate the loan costs properly and don't change your mind in the future. :)