1) I do not have ToA (I play DA), but others who have posted here have reported that ToA nerfed focus, presumably to make it less attractive.  That is, the amoount gained was reduced and/or the amounts in the other areas was reduced.

2) Yes.  However, one variation of all factories, especially when the homeworld comes with a juicy (3x or particularly 7x) tile, has you start with rush buying one research building for that bonus tile.  Then, you throw resourses into research until the basic set is achieved, and then you revert to all factories, including building over that research building.  Be advised, there is a limit on the number of techs that can be researched in any one turn.  IIRC, the number is the # of colonies + 1.  Hence, you may not be able to use all the research you get very early until you settle a few worlds.  It is partly for this reason that many recommend converting the initial miner to a colony ship at the start.

3) Yes, same for morale.

4) Yes, the most common setting seems to be 1-99-0.  (Note, for the scenario in #2m the sliders would be adjusted every turn until reverting to all factories)

If a player has a high research output, s/he can gain in one turn multiple techs in the same line.

For example, suppose one has been playing for a while in a game and suddenly decides to research (say) beams.  You select "beam theory" (you already have done, say, guns).  The next turn you may get the message that you have gained beam theory, laser 1, laser 2, and laser 3 - four tech levels.

Early in a game, even if you have huge research, you can get only the number of advances equal to your colony count plus one, IIRC.

Thus, if you do not convert the space miner and quickly colonize the two planets you can without building a new ship, you are limited to the # of advances per turn you can get in research.  In some All Labs strategies, this can be crippling.  Actually, in any strategy that devotes most of the first ten or twenty turns to basic research, it can hurt. 

Yes to all.  I have been playing all factories in ToA and still find it viable.  I have read that in ToA focus diverts 20% rather than 25% of your output but you still pay for the 25% but I have not done testing to confirm.

A late reply as I haven't been browsing this forum for a while.

To set focus on one of your planets, double-click the planet, then look at the top of the screen where you see the hammers, some other symbol and the beakers. Then left-click either of these 3 areas to put focus there. You'll see the numbers next to the hammers and beakers change + the selected area will be lighter in color. To change back, click the same area once more.