I'll start with the Commander questions, since they're the easiest.

#2
In a non-matrix army, such as Orks, there is 1 overall Commander/Leader. In this case he's called a Big Boss. My plans for him are to create a unit with him as the only member and make him a level 1 or 2 commander. This will gain me an extra activation card(s). If another one of my units has several broken figures, can he join that unit to help with individual rally rolls? This would mean 2 units have now joined together.

A Primary Commander IIRC must be chosen as part of a standard unit, ref page 14 "How Units Activate" subheading "Primary Commader". HOWEVER he can leave that unit the start of any turn, and freely join another unit at the start of any subsequent turn: ref page 19, "Commanders" for more details. In other words just roll with the standard rules on this, they're quite close to what you want.

EDIT: I'm pretty sure you can legally create a standard unit that is just the commander. That uses up one of your 15 Standard Units. But, you really don't need to. But, I wouldn't object to an opponent doing that, anyway.

#3
Continuing with the above situation. Say the commander is allowed to join another unit. When would the combined unit activate? When the commander's unit card is drawn or the other unit's card?

When the Primary Commander joins a unit, they use the same activation card- remove the Commander's Activation (not Command) card from the deck. When he splits from a unit, they go onto separate cards again, so put the Commander's Activation card back in the initiative deck.

On to the Matrix questions:

#1
The Games Workshop 40K Tyranid army is a great fit for a Matrix style army. The basic troopers (Termagaunts, Hormagaunts, Gargoyles) are all matrix units. The Tyranid warriors and the Hive Tyrant are Focal Leaders. My question is, how do I assign Tyranid warriors to lead Termagaunts? I think the answer is to create Ad-Hoc units. For example, combine a unit of 10 Termagaunts with another unit of 2 Tyranid warriors both of whom are Focal Leaders. Is this correct?

While correct it may be sub-optimal. If this helps, a Focal point is not necessarily a Leader, it just indicates that the group intelligence networks through a particular node. I'd just allow Focal Points in any Matrix unit; it could mean that the Hive Mind happens to be focusing some attention on that swarm at this moment.

Otherwise, yes, Ad-Hoc or mixed-frame and therefor Exclusive units would be the go IMO.

I saw the Organic/Biotech and Space Thugs army lists that Demian published.  It's close to what I want.  It's only the leaders and focal points that I'm considering tinkering with.  I just want to make sure I completely understand the rules before I do so.

I've understood the net effect of the Commander rules to be that while a Commander must be chosen from an organizational Standard unit in order to be designated as the Primary, the said Commander can be fielded as the sole member of such a unit (pg. 19). It is technically permissible to assign a unit slot to house a Commander if you like (as per Organic genre Queen frame), but I don't think it's absolutely necessary in order to field an individual PC. So I think one can have all of the possible combinations: a PC without a designated (or fielded) "retinue", a PC with a designated but not fielded "retinue" and a PC with both designted and fielded retinue. What you can't have is a PC with an ad hoc "retinue" created on game to game basis.