Washman - Let me start off by saying that I am not an accountant, but I will tell you that I too have a similar situation. I have a very successful S-Corp, a car wash that is an S-Corp, and multiple LLC's (12 or 13).
I would first suggest that you find a really good accountant if you've not already done so.....preparing your own taxes in the situation you've explained is not a good idea. I wouldn't necessarily consult with a CPA (not saying their all bad, but most of them will cost you money). I would find an EA (enrolled agent). EA's are virtually identical to a CPA less all the red tape and annual certifications that govern the designation. This means they have more opportunity to explore the gray areas of the laws than a CPA.
If you're C-store is indeed a C-Corp, I would suggest speaking with the accountant or a tax attorney about changing it to an S-Corp. It is my understanding that income generated by a C-Corp is transferred directly to the owner(s) as income, whereas in an S-Corp the tax liabilities transfer to the corporation first and then profits minus deductions are issued to it's stockholders via a K-1 Dividend. As you could imagine the opportunity to benefit from tax deductions are much higher for you the stockholder.
It may not be a bad idea to then set-up another LLC that your wife manages and operates. This LLC can bill the S-Corp for her or it's services (which is a tax deduction). Anything she needs or purchases for her to operate her business is then a possible tax deduction under the rules of an LLC; i.e. automobile lease, computer, supplies, office furniture, software, etc.
I know nothing about Rental Property and the tax laws associated with them, but I find it strange that you wouldn't be able to benefit from the passive income produced by the LLC.
Once again, speak with a professional. I would venture to say that if your not getting this type of advice now you should consider finding someone else.