Buyout results in negative ending partner capital

Ok.  We are ready to go.  Partnership tax is complicated and this type of a forum is not really the best to handle this type of issue, but I will provide some general advice and comments.  You have a fair amount invested and it may be in your best interest to meet with a tax profession so you can have a one on one discussion here.

• The first thing you need to do is reverse the $90,000 adjustment you noted in one of your responses.  This is completely incorrect.  
• As a member in an LLC, you need to be maintaining a basis schedule of your investment.  Attached is some commentary from the IRS on how to maintain your basis schedule https://www.irs.gov/instructions/i1065sk1/ch01.html
• The $90,000 you paid your partner will be added to your basis schedule; this is your outside basis (tax basis).
• Since it appears that you may have paid your partner some goodwill, you will need to determine if the LLC should make what is known as a Section 754 election (step-up).  This can be complicated and beyond the scope of this forum, but it essentially is a worksheet that compares the tax basis of what you purchased  to the FMV (your purchase price).  The difference will become your step-up. Why this is difficult is because you technically bought an additional interest in each item of the LLC.  You can group it, but it will still take some work.
• The reason this is important is that if you did pay more for the interest, by making the Section 754 election at the LLC level, the LLC will be able to specifically allocate additional depreciation or amortization (goodwill) to you as a result of this "step-up".
• The LLC should put this step-up on the asset detail, depreciate or amortize it and as noted previously specifically allocate this to you each year.  This will be separately stated on your K-1 line 13W noted as "Section 754" deduction.
• If a Section 754 election is made at the LLC level, you will then need to attach a Section 743 statement to your personal tax return.  This schedule will detail to the IRS how the step-up was determined.
• The capital accounts on your books and records of the LLC are "inside basis" figures.  To eliminate the other member's capital you will just reallocate his capital account to the remaining member's in proportion to their new ownership.  
• Your former partner, who should have also been maintaining a basis schedule. will update his basis schedule for the final K-1.  He will then compare the amount you paid him to the basis schedule and determine his gain.
• This will also add some complexity.  Since he technically sold his share of all partnership items, some of the gain could be recharacterized as ordinary.  This would be the result of his share of what is called "hot assets".  One such item is his share of depreciation recapture.  The LLC will need to provide some assistance to him in this area.