1) Do you put each property in a separate LLC? Also, do you have a separate "main" LLC that each "property" LLC pays too
We use a WY-based asset-holding LLC as the "main" LLC, and separate state-based LLCs (including MO, since we also own in KCMO) that are then owned by the "main" LLC. Each property does not have to be in a separate LLC; that is up to you, and is based on your risk tolerance vs the pain of having separate bank accounts, meeting minutes, etc. for each LLC. You can also see if series LLC is available in MO.
One other option you may consider is using revocable living trusts for your conventional financing needs. Offer much the same protections, conventional conforming loans can be done to them, or you can just get financing in your own name, then transfer title to the trust (which is protected by federal law).
2) I know all about tax depreciation and what not, but what is the biggest difference in taxes when a property is in a LLC vs personal name
LLCs are usually pass-through entities for tax purposes, so they don't really affect the bottom line. LLCs are primarily legal entities.
3) have you had difficulties in refinancing when a property is in a LLC and have you had conversations with your lenders when you transition the property
Depends on the type of lender. Conventional/conforming will most likely require you to first deed the property back to yourself, and there are differing seasoning requirements on that. Commercial/portfolio lenders often prefer it in an LLC, but those are more flexible and more expensive usually.
4) Do you get each LLC insured or is there a umbrella policy?
Each property must be insured, and the associated LLC on title also needs to be on policy. A commercial insurance policy can cover multiple properties with different entities. An umbrella policy is usually separate, and provides coverages above and beyond the landlord policy.
5) are there any unexpected costs or annual fees you didn’t expect?
Depending on your state and how you structure things, there may be fees for registered agents, renewal costs, etc. If you have an attorney handle everything to keep it buttoned up, that will inevitably come with costs as well.
6) Does anyone deal with putting rent income into a whole life insurance policy
We use WL insurance policies, but don't necessarily feed the income directly into the policies. I would think you'd simply be taking the rent as a disbursement, and then putting it in yourself.