Many of the topics you refer to were already discussed in this forum over the years. Thus I encourage you to use the search function (above right) and read as much of it as possible. I give a few hints in short below:
I understand I have to get a german visa first to stay yearly and then after 5 years may have the ability to stay longer term?
You do need a residence visa to move to Germany. Normally (but not always) this is to be renewed yearly - but shorter or longer periods also exist (you seem to be at the mercy of the processing officer here),. Whether you can get a permanent one after some time depends on various factors - and I think you should not worry about it now.
What are taxes like in Germany for a retiree who is not working?
1. how would I be taxed by Germany as a US citizen who wishes to live in Germany and holds funds in stocks and bonds?
You will be income-taxed on your world income (from any source) at the normal income tax rates. Making the compulsory yearly tax declaration will be complicated in your case - better engage a tax adviser to prepare it for you!
How about healthcare?
4. How do I obtain health insurance?
5. How easily can I get access to urgent care such as a hospital that does heart stents or provide good stroke care if I have one? How about management of rare diseases- for example my wife is on Humira for a rheumatologic condition called plaque psoriasis with psoriatic arthritis?
This topic was exhaustively covered in other forum threads. In short: Above 55 years of age, the public scheme is closed to you and the private scheme will be costly (plus pre-existing consitions like your wife's may be excluded).
Health care in general is very good.
2. Are there local and state taxes on top of federal?
No, not on the income tax.
3. Are there property taxes? Are they only on the sale and purchase or are they yearly and how much?
There is a tax (locally differeing between 4% and 6.5% of the price) on roperty purchases and a yearly property tax (small - not more than a few hundred Euros per year). Other necessary fees, at buying time for agent, notary public and land registry, and yearly for garbage, road cleaning, etc. will be higher than that.
4. If I were to work how would I be taxed working for US clients over the internet and phone in Germany? What if I lived off a combination of consultant income and my investments?
There is no difference between foreign and locally sourced income - just the declaring procedure (and potentially accountancy requirements, since you will be classified as self-employed) will be more onerous. There are, however, many rules (registration, accountancy, etc.) that make it difficult to be self-employed.
5. What would my estimated tax be off my investments? Off a consultant income that paid 88k USD?
A first indication is available by online income tax calculators (see links in previous threads), but for a definitive answer ask your tax adviser!