[Thermal shields and early warning system / obstruction]

Thermal Shields takes place first, "after gathering", and obstruction takes place "before rolling".

[Salvo attack against Emperor Palpatine officer]

Yes.
As a note, you'd spend the defense token for Emperor Palpatines (Officer) effect when the Salvo attack begins, not when you spend the Salvo defense token.

[Moving out of the play area and measurements]

You measure from the final position of that ship or squadron.
If you do not have a physical space to place the ship or squadron, do your best to estimate from where its final location would be located.
 

[Hot landing and Reserve Hangars Deck]

Yes.

[Hyperspace Assault and Mercy Mission]

Per "Effects Use and Timing" the player chooses the order in which effects are resolved when they share the same timing.
So,
A) Yes. 
B) Yes.

[Reactive Gunnery timing]

Yes. Reactive Gunnery resolves in the "Spend Defense Tokens" step.

[Engine Techs and overlapping station]

Yes, however this only applies to Unarmed / Armed Stations.

[General Grievous (Commander) + Reserve Hangar Deck]

1. Yes

1.1. The squadrons position where it was destroyed.

2. Yes.

[Nevoota Bee]

Yes. Non-unique squadrons that Nevoota Bee activates gain the "Swarm" keyword for their activation and are able to reroll a die when attacking ships.
 

[Yularen and dial+token resolution]

Yes.
For example, spending a squadron dial and a token would mean a ship would resolve its Squadron Value amount per the spending of a Squadron Command dial, an additional One from a Squadron token, and also another additional squadron from Admiral Yularens affect.

[Salvo and Ackbar]

Quote

"Before a friendly ship's Attack Step, it may choose to attack from only its left and right hull zones this round. If it does, it may add 2 red dice to its attack pool while attacking a ship."

A ship can only choose to resolve Admiral Ackbar's affect during that ships activation (See "Ship Activation" Topic), before its "Attack" step.
A player cannot choose to resolve Admiral Ackbars affect before its appropriate timing window.
Attacks made by that ship earlier in the round wouldn't prevent a player from choosing to resolve Admiral Ackbar effect at the appropriate time.
 

[Iden Versio interaction with 1.5 Evade Rules]

Yes, Iden Versio would cancel 2 die in this instance.

[Tikkes and Raid Tokens]

Yes, per "Effects Use and Timing", a player can choose the order in which to resolve effects. 
For example, you can resolve Tikkes affect to gain a command token of your choice, and then use choose to discard that command token to discard a matching Raid token in the same timing window.

[Can you choose not to ready an upgrade card when you have the ability to do so?]

You can find this answer in the Star Wars: Armada Rules Reference in the topic "Readied".
Relevant part bolded.

Quote

 

• While an upgrade card that is not marked with the Recur icon or Non-Recur icon is exhausted, that card is treated as if it has the Recur icon and is readied during the Status Phase.

◊ This includes upgrade cards printed prior to the introduction of the Galactic Republic and Separatist Alliance factions, which are not marked with either icon.

 

Also in the "Upgrade Card" topic,

Quote

• Upgrade cards are readied during the Status Phase.

Also in the "Status Phase" topic,

Quote

During this phase, the players ready all of their exhausted defense tokens by flipping them to their readied side. They also ready all of their exhausted upgrade cards by rotating them 90° counterclockwise. Then, the first player flips the initiative token to its other side.

in the "Ready Cost" topic,

Quote

◊ Command icons: The owning player can pay the cost by spending the indicated number of each type of token shown.

An Upgrade Card that does not have a ready cost, is readied during the Status Phase. A player must ready an Upgrade Card that does not have a ready cost unless otherwise prevented.
Upgrade Cards that have a ready cost are optional to be chosen to pay the cost to ready them. A player is not forced to ready them if they do not wish to do so.

[Exhausting an unmarked upgrade card]

Yes, you can "exhaust" an upgrade card that does not have a recur or non-recur icon.
An upgrade card that is "exhausted" has its effect in play as specified on its upgrade card unless otherwise prevented.

To put another way, "exhausting" an upgrade card that otherwise wouldn't "exhaust" such as XI7 Turbolasers, has no effect on how that upgrade card resolves its effect.

[Obstacle movement and tokens/Mines.]

No. The token is considered part of the obstacle that is moving, thus, the token also cannot end overlapping another object.

[Gilded Aegis question]

Yes, Gilded Aegis can resolve more than once per round, but it can only resolve in the timing windows specified on its upgrade card and if it has a Redirect Defense Token to discard.

[Nova defiant clarification]

Nova Defiant is still restricted to only holding 4 command tokens per its command value.

[Lumina unduli and admiral Sloane interaction.]

A defense token that is spent by an attacker is not considered to be a defense token that was spent by the defender. 

Luminara Unduli would resolve as long as the defender spent fewer than 2 defense tokens, but you can not ready a defense token spent by the defender.

In your example, if an attacker spends an "exhausted" defense token, it would be "discarded". The defense token cannot be chosen to "ready", as it is discarded.

A defense token which was "readied" and spent to be "exhausted" by an attacker, can be chosen by the defender with Luminara Unduli effect to "ready" and returned it to its "readied" side.

[Is a squadron in close range if it's within range 1?]

Yes, a ship would be able to use Point Defense Reroute affect when attacking a squadron at close range.

[Question regarding Counter]

The dice to be used in the attack would be black due to the Flak Guns effect.

[Invisible Hand Range]

Yes, Invisible Hand is limited to only be "within distance 3" and no other range band when deploying squadrons.

[Star Wars Armada: Frequently Asked Questions]

Question: For B2 Rocket Troopers, Does the attack itself have to be at close-medium range in order to use the effect, or does the range to the enemy ship need only be close-medium even if the attack itself is at long range?

Answer: B2 Rocket Troopers may only be resolved if the attack is at close-medium range.

[Luminara Unduli and Spending 0]

Yes, Luminara Unduli's card effect is able to be resolved if 0 defense tokens are spent by the defending ship or unique squadron.

[Star Wars Armada: Rules Reference Corrections and Useful Links]

Rules Reference Correction: In the "SET ASIDE SHIPS AND SQUADRONS" topic:

New changes for this topic in blue.

To look like the following,

SET ASIDE SHIPS AND SQUADRONS
Some effects refer to ships or squadrons being set aside, typically before the “Deploy Ships” step of setup. The player controlling the set-aside ship or squadron places it outside the play area near its ship or squadron card along its player’s edge. These effects specify when those ships or squadrons can be deployed later in the game.
• A ship or squadron that is set aside is not in play and can only be deployed or affected by the effect that set them aside.
◊ When a squadron that was set aside is deployed, set its activation slider to display the same color as the initiative token.
• A set-aside ship or squadron can only be assigned objective tokens or chosen as an objective ship if that effect is resolved before the effect that sets that ship or squadron aside.
• If a player has set-aside ships or squadrons remaining but all of that player’s ships in the play area are destroyed, the game immediately ends.
• If a player has set-aside ships or squadrons remaining but the game goes to time, or the end of the sixth round their ships and squadrons that are set aside are destroyed.