I'm not a heating engineer, just a guy that has installed a few coal boilers and learned some things along the way. Here are my thoughts:
I want Pri/Sec w/ pump zoning...2 zones.
Primary/Secondary is normally used when there is a mix of high and low temperature radiation (baseboard, radiant, etc)...but there is no reason you can't do it here...it will just use a few more fittings and an extra circulator.
When to get rotated flange and why???
You can use either style when installing new components...if you have an existing header that needs a circulator replaced, you just need to make sure you get one that is the same style.
How does sizing the pipe effect choosing the matching pump later??? Doing it smart...is bigger better???
Generally speaking, the larger the pipe the smaller the pump that is required to have a given amount of flow. You don't want to go so big that the water velocity in the pipe isn't enough to move the air bubbles. 1.25" will be fine for the primary loop on your AA130.
Integral valves in flanges...is it worth the money for a do-yourself install???
I think so, they make changing a circulator a snap.
Which by-pass...boiler by-pass???...how fancy or simple does it need to be??? how do you size it?
If you want to pipe the boiler in a primary/secondary fashion, I would skip the bypass. The high flow through the primary loop will help prevent thermal shock, and when the boiler is sitting idle there will be enough gravity circulation through the primary loop to prevent stratification in the boiler.
How important is it to keep secondary loops short...does it just come down to economics or are there other factors?
It is mostly an economic decision. Naturally the longer the run the more pipe you have to buy.
A longer run of pipe may require a larger pump to move the btu's you need...or not, it depends on the load and the diameter of the pipe.
What do you think of 3 speed pumps???
I like them.
What do you think of Outdoor Resets on solid fuel?
Never tried it...I just adjust the aquastat on my boiler a few times a year.
What other tips might you lend...what would you do different if you were doing another today?
Pipe the boiler and zones so they can easily be power-purged from the basement...pump away from the expansion tank...use a commercial floor mounted expansion tank...pipe the headers off your primary loop so more zones can easily be added later...use "tees" instead of elbows in your flue pipe so it is easy to clean...and lastly, use anti-seize on all fasteners.
Edit: I attached a diagram that someone was kind enough to post on the heatinghelp forum a few years ago. You can use 1.25" piping instead of the 2" referenced in the diagram, but it shows you the general idea.