Can I take my profits from trading and make a KEOGH/SEPor other pension plan contribution?
Unfortunately, profits from trading are not considered earned (although we know they are tediously and laboriously earned) income.
On the positive side, these profits from trading (whether as a trader or Mark-to-Market Trader) are not subject to self employment tax. I believe this may change in the future, but the above information reflects current tax law.

I never filed a Section 475 election for 2016. Can I take my losses in full or am I limited in 2016 to a $ 3,000 deduction?
Unfortunately, the election for calendar year 2016 had to have been made by 4/18/2016 and there are no specific exemptions from that requirement. It may be possible to request relief and exemption from that deadline but there are no suggested procedures as to how to do that. An expensive and time consuming letter ruling can be requested or perhaps just a letter requesting exemption could be done. At this point in time, it is unlikely the IRS would grant relief after a full year of trading results have been realized. A taxpayer should assume they will not be allowed to file as a MTM trader for 2016 and definitely be sure to elect for calendar year 2016 by 4/18/17.

How does Section 475 effect wash sales?
One of the great benefits of electing MTM Accounting by making a Section 475 election is that you are exempt from any wash sale reporting requirements. Since any gains on positions are marked-to-market and recognized at year end, the IRS concerns about recognizing losses in the current year while deferring gains into a future year are eliminated by the application of Section 475. Since traders frequently trade in and out of the same stock frequently, intraday or within a short period of time, this is one of the great reasons to elect Section 475.