I will take a swing at this, but since its been a couple of weeks, either you have figured it out for yourselves or found a better way. Anyway here it goes...
What sort of strategies should the remaining 2-3 players have?
If you are playing the hardest AI levels then your remaining teammates should be securing planets and protecting borders. Secured planets can be handed over to your teammates that are trying to build up eco and tech fast so you will have their support late in the game.
Is it acceptable for a team to have 2 boomers to supply them, or to have 2 Vasari RA rushers?
Well, you mentioned about that you don't like rushing and you like the long games. Do what ever fits your team's profile the best.
What sort of order should the three race types progress through research very early in the game?
This will be more personal peference than anything else. Obviously your mates that are focusing on eco and that will supply the team later should focus their research for that purpose. everyone else should either build up fleet power or fleet enhancements since they will be protecting the combined empires.
How rapidly should you expand?
depends on how long you want your game to last. if the hard and unfair ai's are teamed up then you want as many planets as you can get right off the bat. otherwise you will not have the infrastructure to fight them later in the game.
When building large armies on each of the three teams mid to late game what sort of ship compositions should they be made out of?
to each his own. since you are fighting the ai, mix things up. each person focusing on a different type of ship will make things boring.
How do each of the teams rank in capital ships, and what capital ship type would you personally recommend on each team?
i would expect to see people that are fleet intensive with more battleships and carriers while the eco people might have colonizers. again for your fleet to be most effective things need to be mixed together. most caps are best when supporting fleets rather than leading them.
For each of the teams, how would you recommend going about setting up trade routes and refineries?
trade centers and refineries at every planet. especially for your TEC members.
Are refineries worth it?
like trade centers, they are not worth their cost early in the game. as the game progresses you will want the little bonus they provide.
Sorry about all of the questions, but I was rather curious about strategy in this game.
whew...gimme a minute while my fingers cool off.