I would assume Jan only affects the first attack. I am trying to put jan with an outer rim smuggler (a very underused ship)

her ability states when attacking may roll 1 additional attack die.

Gunner states you make another attack if the first one does not hit.

However marksman has the "for the round" clause

Jan does not have the 'for the round' clause. In fact, when her ability is used, she is immediately given a stress token. Her ability does not work when she has a stress token.

So it works something like this; you use her to add a die to your first attack, she takes a stress. The attack resolves, misses, and Gunner kicks in. You check for Jan's ability, see that she now has a stress token, and are unable to use it.

I broke it down into the steps and now i'm a little confused on when gunner would kick in.

Gunner Triggers after check results and before the deal damage step, after you make an attack that does not hit meaning after check results you trigger gunner.

if this is the case then vader or any other similar ability would happen before the deal damage part (completely redoing how vader is used).

I do understand the part about where she would be stressed you could not add another dice due to checking.

Well, they function a bit differently. Gunner kicks in after perform an attack that misses. Vader, after you perform an attack, period. I think in both cases they trigger after the initial attack has been completely resolved.

i Would assume so but it made my head hurt thnking about it differently.

Gunner doesn't trigger until after the attack has completed. It depends on whether the attack has hit or missed, which is determined during Step 6, but you haven't actually performed the attack until it's fully complete.