Keith, you have a lot of good knowledge and appear to think very rationally, so I think it's a shame that people immediately write you off, but I do think you're missing a few key pieces of assumptions in your analysis.
1. A lot of the posters making this point, and it's true - you can't account for all of the factors that influence market pricing. Many people have tried to fit things into a pretty equation, and it just doesn't work. You know this to an extent becuase you have your own business, vacancy is never what it's underwritten as, nor is maintenance/repairs. Well, for real estate, there's a lot less variables than the stock market because psychology and emotion doesn't come into play daily. The illiquidity of real estate helps in this regard because you can focus on the underlying cash flow. Another example is the profit margin point you are bringing up - what makes you think it will revert to the mean? And if it will, what makes you think the mean of 6.5% is correct? Businesses should be getting more and more efficient now (hence not a lot of companies are valued by P/B anymore) due to stealing good business processes/practices and rise of technology, and if the government starts deficit spending again, or if savings rates decrease, the private sector will benefit - are you saying that you will be able to predict both?
2. In your analysis, you seem to repeatedly harp on "today's" conditions. That demonstrates a real estate investor's line of thinking. Unless if you buy at a severe discount, real estate has capped potential. Buying a piece of real estate at a decent cap rate (let's say 10%) or at a fair price, is different than buying a piece of business at a fair price (let's use your example of 15.5 PE). Although the underlying earnings is higher on real estate, rents (and subsequently, total price) increase extremely slowly, historically at the rate of inflation, whereas the best businesses grow earnings at a rate that handily beats inflation. So to say "ignoring growth" isn't a fair, apples to apples, comparison. There's a reason that stocks have trounced treasuries so handily for 30 years even though long term treasury rates handily beat the earning yield of sp500 at the end of a lot of fiscal years (you can do a comparison using
http://www.multpl.com/10-year-treasury-rate/table/by-year and calculating the earnings yield for SP500 from the same site).
3. Opportunity cost matters, and this is a reason why the Shiller PE's usefulness can be overstate, imo. By measuring Shiller PE as an absolute measure of expensiveness, you assume that alternative investments are always yielding the same amount. But logically, if Treasury notes are paying 10%, stocks *must* then be priced at 10 PE or less for it to be a fair deal, after accounting for the effects of growth and inflation. Currently, with ten year treasuries paying 2%, a 5% earnings yield on stocks is a pretty good sized premium (plus the 5% earnings can grow 7-10% at even the largest companies). You already mentioned this, so I'm confused as to why you haven't made the connection between low treasury rates and why an "inflated" Shiller PE can make sense. You can always invest in real estate, but again, you're probably capped in today's environment to ~8% cap rate, which can grow at 1-2% with inflation (not much inflation right now). Real estate though, has the advantage of structure, since in the US, you can leverage with fixed debt. The other perfectly good option if you are patient is to hold cash, and pick up assets once they become reasonably priced to you (either through a crash in pricing, or through stagnating pricing until earnings catch up)
EDIT: It's also odd to me that you say: "
VDE has a 22 TTM PE right now in the middle of an energy crash. As is, this implies a return of 4.6%. However, I believe the last 12 months of earnings are not representative of what earnings will be in the future. They are obviously depressed. I expect them to be higher in the future which will push the pe back down into my comfortable range of 15 to 17 or lower which should safely give me a ~7% return or better, maybe much better, long term." but accept Shiller PE as a definitive measure, when PE10 includes 08-09, dramatically and temporarily reduced earnings for the entire US
For all of these reasons, the many factors governing the stock market, the growth component in stocks, and opportunity cost of "risk free" treasuries, I think the stock market isn't too overpriced currently. I do think that there are spots in the market that are making it seem that way, such as a lot of the consumer staples and (worst offender) start up tech/social network companies. Energy seems to be undervalued, as well as some financials (investor wariness still) and older tech. But overall, the market seems to be fairly priced.
In the end, I think you are very knowledgeable, but have some misunderstandings about how macro predictions actually affect the market - there's a lot of knowledge out there tho, and life experience is the best of all, since you seem to have a pretty good underlying economic engine (real estate business), I would say that my only advice to you is not to over do it, be conservative in how large your bets are and you should be fine