Regarding point 2, I'd say the variation as shown by Forge World
is the official line. If pressed, I'd say that the only "standard" Marine shown in the book is Battle-brother Raban of the third company (page 58). He has all-over gunmetal armour, with the company number on the right knee. Having said that, the example shoulder pad on page 55 has a blue field and gold surround, so perhaps Brother Raban is just in "low-contrast" armour with minimal decoration.
When I get round to doing mine, gunmetal with blue shoulders and gold edges will be the "standard", but that the Astral Claws (and Marines in general,
IMO) have a wider range of permissible heraldry variations than commonly shown by modellers.
I addressed point 3 in passing; a roman numeral on the right knee, perhaps? Having said that, the vehicles show the company number as an arabic numeral, and Veteran Brother Amru on page 55 has an "IV" despite being in the 1st company, so perhaps that's the squad number? Who knows. pick your own system, and remember that not every model has to be marked in exactly the same way.

I think I'll be treating that number on the knee as the squad number.
I can't tell what that "throwing star" icon on a lot of the Astral Claws is - a campaign badge, perhaps?
As for Chaplains, Huron had plenty of time to implement his ... reforms before the Tithe fleet was fired upon in 901.M41. Presumably as he built up his Tyrant's Legion, any dissent among the officers was dealt with - any Chaplains in the Chapter by this point would have been on-side with Huron.
p.s.; I'm not normally egotistical enough to Exalt my own posts; I clicked the wrong button.