I am happy if my experience is helpful to you.

Embrace the randomness :D It is wonderful.

B: After you use a feat, the player must make a save with the relevant stat (Smite VIG, Focus CLA, Deny SPI). If you fail the save, you gain Fatigue and you cannot use feats until you take a break (end of combat). My players were quite careful with the usage of Smite, because Deny is a very strong way to save the knights life. I think Focus is quite weak I didnt touch it, but I consider to homebrew it that gambits purchased with this feat are considered strong gambits.
It may depends on the players, luck and the myths you use, but my experience was that the monsters are not hard enough :D I buffed up some of the creatures :D Like I gave the wyvern an ability to regain its Guard every time it is spends a turn in the sky without attacking and taking damage (I also telegraphed this mechanic to the players so they can make informed choices!!!). Later I started to use a homebrew rule for large creatures - Some of the monsters can be harmed by only blast damage or by spending a gambit on scaling up the effect. I gave an npc the ability to always have 1 extra movement, etc.
Also I think most of the time I used battlemaps for the combat (I like cinematic, tactical combat with exciting environments) Nothing fancy, I drew some sketchy maps on the go and used my pretty little glass pearls, that way it was always clear what a blast attack can reach (everything your pearl touches)

C: You roll travel at the end of each Phase spent in the wilderness. You do not roll for Omens when you are in a holding. And no, you do not progress the Myth. They happen when the players encounter them. The only time when you tinker with the progress of the omens when the players actively search for the myth. The example in the book is about players searching for the Wyvern's nest, tough I never really had to make any modification in the order.

D: The players rolled for travel, I didnt explain them the exact method but after a while I think they kind of recognized a pattern: The higher the roll, the more boring the travel is :D
I did not use any other kind of encounter table, but I used some stuff from other myths that wasnt part of the campaign - I used npcs and their inventory from other inactive myths, like I introduced a grim kind of savage npc and I used an npc from the Axe myth.
It is not considered an encounter, but when they rolled "all clear" during travel I rolled up some ideas from the spark table (sometimes out of game when I had an idea for a location or a moody phenomena I noted down and then used in a random place during the game). Of course I always described the details of the environment, but when all was clear, I let myself a little bit more time to do so.
I used the example adventure site from the book, I improvised one during a lunchbreak. I actually prepared another between sessions, but they never visited the place :D great lesson.

E: We didnt have a session zero, but when we created the characters we discussed the setting, the culture, the society, the role of the knights and the seers. Actually I think the biggest change we did before even started to play the game was in the Oath. We didnt like the Seek the Myth part. We felt it was too meta, too gamey. We changed it into Seek the City. I imagine it is not a necessary thing for a lot of table, but it worked for us pretty good. They did asked about and searched for the seers in the realm. My players are quite experienced and are eager to immerse themselves into the setting (That is the reason why we discussed for like at least an hour the oath and the knights' place and role in the society). Based on the seers annointed the PCs, the players had a pretty good grasp of the - sometimes inhuman - nature of the seers, but I try to enforce during the game the weirdness of these npcs. If you take some advice, be super weird when you play the seers, The description of them are pretty useful, but be ready to incorporate some random elements. They met the Hanged Seer in the crossroads, the naked ascetic man, with strange encarvings in his body tried to hang himself desperately on a tree. The knights helped him out. Sometimes I rambled random bullshit, which kind of foreshadowed omens from myths they didnt encounter yet. (EDIT: The little poems of each myths are really helpful!) It helped me and the players embrace the out of time and place nature of these strange creatures. I also used the Salt Seer, who cannot even speak, if the characters lick his salt, they gain strange visions. It helped them out, one of the character took some salt with him and later when they left the sanctum asked advice from the seer by eating the salt.