Let's think about this for a minute. One of the allegations is that Trump used the foundation to buy a Tim Tebow autographed helmet for $12k. Anybody can buy one online for less than $1000. That begs the question of why ANYONE would pay $12k. The answer? It was purchased at a charity auction for the Susan G Komen Foundation. The contention is that this deal somehow "enriched" Trump personally. Please explain to me how paying $12k for something only worth $1k amounts to "enriching" yourself or your organization. If the Trump Foundation paid for the helmet then it belongs to the Trump Foundation, not Donald Trump. Maybe...possibly....perhaps if Trump took the helmet and displayed it in his own trophy room it might be considered to be "self dealing" but even then at a value of less than $1000 it's not much of a deal.
As far soliciting donations from others and then passing those donations on to others goes that isn't the least bit unusual. Have you ever heard of the United Way? That's what they do. The difference is that the United Way keeps 10% or so of the money you send them and the Trump Foundation doesn't.
Regarding the flag pole dispute, here's the story -
Trump settles dispute over flag - tribunedigital-sunsentinel
The fines were waived with the agreement to make a donation to a veteran's charity. That's true. What's also true and isn't cited in the absurdly biased article you linked to is that Trump also dropped his $25M suit against the city. That seems pretty fair to me.
With regard to using charity funds to buy portraits of himself, these are all charity events. There's no "enrichment". When you buy a $250 painting for $5000 the only one being enriched is the charity that's selling the painting and that's the way it's supposed to work!
OK, I knew there was one I was forgetting. Trump contracts to give a speech then waives fees as long as the organization he's speaking to makes a donation in the amount of those fees to a charitable foundation. The organization chooses the Trump Foundation. The contention there is that Trump should have to pay tax on that fee even though it went directly to the charity. As long as Trump didn't say "you have to donate to my charity" and as long as he didn't then use the donated funds for his own purposes that's perfectly legal. In fact, if you parse out the 800 paragraphs of innuendo you get these two paragraphs
As long as Trump never had constructive receipt of the funds and as long as he never dictated where those funds go he didn't do anything wrong.