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The troops are the same, crownlands units for Targaryen faction. The reason for the culture name change is because it's more accurate lorewise.

Would be good enough if it allowed you to hire religious units, there's a bonus in healing skills granted by having x amount of them in your party, and the Red Priests upgrade into some nice Horse Archer units.

Oh well, still some legendary improvement you got your sights on Moose, gl with the project.

About the faction blacksmith, yes whatever faction you chose for your character allows you to access it from the beginning, except Targaryen because they control no lands until they invade and conquer a town with shops. And yes, whatever faction you can raise your relations with past that point will let you access their special blacksmith.

Thenn, beyond the wall has a slaver in the tavern consistently, dunno if he's permanently there. Otherwise NW, gets you less stags but helps boost the NW's forces if you are into helping them.

This looks beautiful, do you have the files ready to import, or are you still working on them?

You can send a spy, not sure if it works for your own castles or those belonging to a faction you're working for, there's also the option to ask a companion to improve relations with a location (probably works better the higher their persuasion is).

If you become king you can change your kingdom's culture (this is mostly only relevant in mid-late game), maybe after doing that you can still get those companions that way. I'll try this in my current game and post if it works.

That too, but if your companions having more leadership than you is only a problem if you become king and make them vassals, otherwise using manual tactical commands bypasses those issues.

Faction blacksmith requires that your relation with that faction be at least 70 points, regardless of your affiliations.

That is a bit hard, in any town that has a tavern, and shops etc. there's this option called faction blacksmith that appears in the town's "trade with locals" menu. To buy faction armour you need to have 70+ relation points with that faction. Also, Stormlands don't have any town in the beginning, Dragonstone has Weeping Town (or maybe it's Stromlands after all) at the beginning, it's close to the Stormlands territory anyway. So, if it's indeed Dragonstone that controls it, you can join the Stormlands as a mercenary, join the army of one of their lords, or become a vassal of King Renly if likes you enough, they sometimes ask you by raven if you complete quests for the faction leader, and help them conquer one town with shops, then when your relation with the faction is 70 or more you can buy their armour at th faction blacksmith of those towns. The travelling merchant thaat pops up randomly in taverns also sells medium tier armour of the Stormlands sometimes.

Some maritime sieges aren't working properly, try looking on the wikia for the manual controls during naval warfare, if that doesn't work you have to resign yourself to doing the landed siege instead.

Try ordering them into division formations (select individual divisions by pressing 1 to 0, 1 is infantry, 2 is archers and so on) order them into the formation you want them to adopt and order them to advance ten paces, or to hold position for example, this has happened to me as well in the new version. If you command them manually like I described here they'll get into position.

Keep it or sell it, though it's not worth much. If you have wildling culture when you made your character you can get a giant companion there. Similarly if your character is northern, you can get a direwolf at a place called Wolf's Den.

The last part of Varys quest (the message) affect anything in the world? Will the daenerys show up? If i agree, may i refuse the alliance when daenerys show up (She not deserves the Throne, i must be the King!!! XD)?

If you chose the characters to be named after HBO's GoT then Daenarys will invade some time after you complete that quest.

The Targaryen faction is then treated like any other, you aren't forced to do anything, you can try to earn the leader's trust and becoe a vassal, join one of the army of one of their lords, or ask them for a job and accept a mercenary contract if they offer it. Usually they offer mercenery contracts right away, and if you have a big number of troops they tend to offer a large sum for the initial contract.