Thanks for the very complete reply!
First and foremost I have realized that the castles I start with are pretty well built. The expense of upgrading them marginally is far greater than upgrading a new castle literally doubling the new castle's levy!
This castle concern was because I have a count of contrazo or something like that who directly controls three counties. My "duke" only controls TWO! So for my first several tries inevitably what happens is that I reform the succession laws. I manage to keep him complacent then my child inherits, can only manage 2 MAYBE 3 estates, my army is suffering from that, the army is also suffering from the warring over Sicily and that's when he and his 4,000 men present me with the ultimatum. Usually I can only assemble 2,500 at that point. I'm learning well that I shouldn't blow all my money on castle upgrades ect. It's better to have 1,000 gold war chest to pay for mercs because that a-hole will come for me. This last game it was his daughter, which was the first time I actually won the war, threw her in prison and stripped a county from her family (she's not getting out either. That effectively neutralizes the problem for years. and their family having two counties instead of three really reduces the threat.)
This also gets me. Succession laws only apply to me? One game I thought I'd be a clever bastard. Murder that obnoxious count forcing his estates to be divided amongst his children and wolla problem solved! Noooope. One child inherited. I have to split my estate around but they get to focus their power? What kind of bs is that?!? Rules for the but not for me huh? Really was frustrating....
I haven't noticed any demesne increase or decrease based upon titles. What's incredibly frustrating is that it seems to increase or shrink based upon purely arbitrary factors. Most of the time Boemond can only manage 3 (as I said sometimes just two...). If I'm lucky he can manage 4. If I'm super lucky I can get the vassals to increase centralization buuuut I do realize that I can only do that with my original ruler. The vassals really seem to hate Boemond every game. Might have to do with me not knowing what the hell to do with one of my estates. I've only recently realized that I need to give it to his underage son. My focus is to keep the estates in my direct bloodline as possible because I'm tired of uppity counts of Foggia who think that they should be sitting on the throne. When someone who has no blood relation does that I can throw them in prison for attempting to fabricate the claim. I often try my best to make sure he doesn't get thrown in clean that way I can strip his title as a traitor. Better to start fresh than to keep a family around who hates me...
I think I have one major question. Outside of mercenaries do you have any suggestion to substantively increase my army? I start out with capacity to field 3k or so provided my marshal is recruiting. Even conquering Sicily I usually can get that up to only 3.5k or 4 at the most.
Ah, right, of course 1066 castles are indeed already pretty built up (and your part of the world has pretty good tech as well). So I suppose there is a bang-for-your buck argument for new castles if you have the demesne limit to spare. But wait until you're in Palermo; an extra barony in Apulia won't do you much good then.
Fired up a fresh game, there he is, Roger, Count of Catanzaro. Yeah, I remember him being annoying.
I tried to stuff him under a freshly created Duke of Calabria title, but since he had more counties than his duke, that didn't work so well and I had to slap him down anyway. You've worked out the solution though, let them rebel, crush them, revoke a title or two afterwards.
Yes, keeping a decent financial cushion is a very wise idea. You never know what the game is going to throw at you.
Succession laws apply to everyone. At the start of the game, Roger has a bastard son and three legitimate daughters, and his counties follow Agnatic-Cognatic Gavelkind. Using the console to kill him, indeed each daughter gets one county as one would expect. Maybe by the time you assassinated him, two of the daughters had died and another bastard had been born, or something? Or Roger might have switched to primogeniture by that point, which is probably more likely.
Be careful assassinating members of your dynasty. The kinslayer traits are bad, and rarely worth the risk. Roger is Robert's brother (or Bohemond's uncle, if the assassination was in his reign) so that's Kinslayer or Familial Kinslayer depending on the circumstances. Better to use Roger as a commander and sooner or later a battlefield duel should take care of him for you. Corollary: be very careful leading troops with your character, heir, or other character you care about (genius son in law, maybe). In my game Bohemond slaughtered dozens of North African mayors in such duels, but he's the only character I've ever had who was consistently successful. And I was sort of trying to kill him off because the game gave him the Celibate trait very early, just after I'd found a nice wife for him...
Spent about 40 years waiting for Guy to inherit - ended up being Guy's second grandson who inherited... A very CK experience, that!
One other note about Roger of Catanzaro - once you take the Duchy of Sicily as your capital, you'll be able to trigger a revocation of Messina from the intrigue menu. Roger will almost certainly refuse, but that's when you beat him down and revoke Messina and another of his counties.
Demesne limit is covered here; a second Duke title will increase your limit by one, a King title will increase it by one more, high (Stewardship+0.5*SpouseStewardship) can increase it (aka, don't ever be unmarried as a ruler), and there are the centralization laws.
For the laws, that may be annoying without Conclave. That's one of the reasons Conclave is considered one of the must-have DLCs (Way of Life is the other). Warning, Conclave is not save-compatible; that killed my de Hauteville game, unfortunately. You can pass laws without Conclave but it could take a while. Vassal relations improve the longer your ruler is in power (that's why Bohemond struggles at first, the Short Reign penalty), and if you grant a title (someplace in Sardinia, or a Calabrian county you revoked from Roger of Catanzaro, whatever) the new ruler will have a nice opinion bonus towards you. And you'll probably be granting newly acquired titles to Content and non-Ambitious people as well.
You should not grant titles to underage sons - you want to control their education and marriage. I usually avoid landing heirs; the prestige penalty is trivial and I don't want them doing anything stupid. I did make Guy the new Duke of Apulia once I had the Kingdom of Sicily title and he reached adulthood and married whatever wife I found for him.
A quick tangent - Sichelgaita is an awesome character, and she is allowed to command armies (which she historically did).
Another random marriage note - Matilda of Tuscany is another very interesting character. She has large tracts of land and is unmarried at the 1066 start date. I wasn't able to make a convincing marriage offer, but in my game she only had one child, a daughter, and that was an easy and obvious marriage for Guy's son. Matilda is worth keeping an eye on - maybe her first husband will die, maybe she'll have few children and some careful murder can set up a marriage inheritance scheme for you, who knows. Much better to take all those provinces without having to fight the HRE for them.
Also be warned that the HRE is very stable and very aggressive in this game. If you see a chance to kick them hard when they're fighting many other opponents, take it. My main regret from my game was not piling onto an early Antipapal War that tried and failed to get the HRE under control.
Increasing your army size - you already know about having your marshal recruiting in your capital. Other than that, just building up your castles as funds allow, keeping in mind other needs (title creating, cushion for emergency mercenaries). If a point of comparison helps, when adding Conclave broke my game, the year was 1135, Palermo's two castles each gave about 2200 men, the other provinces in the Duchy of Sicily each gave about 1500 men, vassal levies from the Dukes of Capua, Apulia, Salerno, and Calabria each gave 1000-1800 men, total character sheet troop strength was 15422, though page 10 of the ledger says 19081 (strongest non-Empire realm on the map).
If Bohemond is King of Sicily, his demesne limit should be at least 4 (3 base, figure at least +1 for stewardship bonus). Once you can start getting those centralization laws passed, that's 5+. Even with castles unchanged from the start of the game, that should be 2*1500+2*1200 = 5400 men. Once the levies have reinforced to full, of course. And retinues will start to be relevant around that point as well. Even if you're only at 4000 men, that's a very solid personal levy already, and should be plenty to crush revolts or do some further expanding.
I've found that the first decade or two in any CK2 game is the toughest part, getting your feet under you as you create all the titles you need (for yourself or as vassals), do the initial conquests in your game plan, and struggle to find money to do much else. As time passes you won't be burning money on titles, your vassals will mostly like you, and you can catch up on building up your holdings - conveniently tech should open up more building options around then.