1. Shiller PE is high, meaning price growth is outpacing earnings growth.
If earnings grow faster than they have in the past, you can get a situation where P/E ratios are exactly the same, but the Shiller PE increases, because faster earnings growth and a fixed P/E pushes prices up while earnings from previous years obviously do not change.
Consider two cases (I'm intentionally choosing an ridiculously extreme scenario to illustrate this property):
A) Companies earn $1T/year for ten years and the stock market is worth $15T in the last year. P/E=15. Average earnings over the last decare are $1T/year so the Shiller PE = 15.
B) Companies earn $1T/year for 9 years and $3T in year 10. Given a P/E of 15, the stock market is now work $45T. Average earnings over the last decade are $1.2T/year so Shiller PE = 37.5
I'm not arguing that's necessary what is happening at the moment, but it's important to understand the different mathematical properties of the Shiller PE when trying to interpret it (and this is putting aside the accounting issues you point out which make comparisons of the Shiller PE before and after the mid-1990s an issue of apples and oranges).
2. More people are leveraging. Consumer debt, auto debt, mortgages, student loans, all growing hugely (see MMM article):
http://www.mrmoneymustache.com/2017/06/20/next-recession/
I don't disagree with this point. All that debt together isn't as big as the bad debt of the housing crisis, but a lot of it clearly is bad debt.
3. Speculative investments are gaining steam. Bitcoin and other cryptocurrencies are created out of thin air and people buy them.
The total value of all cryptocurrencies in existence is something like $100B (an effectively a lot less than that since a lot of that is composed of bitcoins that people lost the private keys to years ago).
Personally I think crypotcurrencies have the potential to do a lot of good for the world economy long term, but the fact of the matter is that at the moment if we woke up tomorrow and every cryptocurrency on the planet ceased to exist, it wouldn't even be a blip on the US economy.
4. Construction cranes everywhere, overbuilding retail, but when you go to these new locations the restaurants look empty. Old malls have tumbleweeds going through them.
Read somewhere an estimate that as a result of consumers shifting to more and more online purchases we likely have more than one billion square feet of surplus retail space that will have to close. However, I do think reason for a lot of the new construction you see in the USA is the ongoing shift towards economic concentration in a few large urban centers. Even if we need a lot less total retail space going forward, there may be local areas where the population is growing fast enough that they don't have enough of it. When I visit places like DC, SF, or ATL and see lots of new towers and skyscrapers going up, it seems like most of that is new residential housing.
5. Hearing stories of my neighbors, friends and family paying astronomical prices for houses, and keeping their old place and renting it out.
I guess my answer to this is pretty much the same as the one above. Some parts of the country are seeing big net inflows of migration and the supply of housing hasn't caught up yet. Other parts have stable or shrinking populations and housing is quite affordable.