Ok, so...would I be right in reading the list as meaning all of Run & Gun is legal(except for actual optional rules, like the
initiative tweaks)? Or is it just some parts of it that are?(like how from Arsenal, only the weapon and armor mod rules were
legal)
So far, that's correct. In Arsenal, the Martial Arts and Advanced Combat Rules sections were specifically listed (in Arsenal, pp. 156 and 161) as optional rules, so they fell under the Missions "no optional rules" rule. In Run & Gun, the only "optional" rules are RG1-6, so basically the whole book (except RG1-6) will be Missions-legal except where called out in the FAQ.
One exception so far is the current rule in the FAQ about gear "healing" itself between missions if you take a week off (p. 12 of the FAQ), which counteracts the "Fixin' All the Broken Drek" rules (p. 143, Run & Gun). I hope that exception stays in place--otherwise, it will become a
lot more expensive to play a rigger and deckers will want to implant their decks to prevent physical damage to them. Given the intent to keep Missions pay low, you
really don't want to pay 10% item cost per box of damage repaired, just for materials.
Crafting is out (p. 10 of the FAQ), so technically some of the explosives chapter (making your own) is out.
