If two passes have gone by and we are using the rules of people coming in late on page 160 of the Core Rule Book.
If a character enters combat after it has already begun, they should roll for their Initiative Score as normal and then subtract 10 for each Initiative Pass that has already occurred. This means they may get an Action Phase during the current Combat Turn or they may not, but at least they have a chance.
Using this method puts us at this set of Initiatives.
Initiative Rolls for current situation. Organized.8-bit | Ghost -
Initiative:
15+3d6 30 | Two action passes have gone by, so Initiative drops to 10
JackVII | Harrier - Initiative: 9+4d6 → [9,6,5,3,6] = (29) | Two action passes have gone by, so Initiative drops to 9
Ericen | Flicker (Using prerolled result, since I cannot find a new roll) - Initiative: 11+4d6 25 | Two action passes have gone by, so Initiative drops to 5
Csjarrat | Morgan - 10 + 4d6 4d6=14 = 23 INI in hot sim. | Two action passes has gone by, so Initiative drops to 3
All4BigGuns | Cutter -
3d6+11=23 | Two action passes have gone by, so Initiative drops to 3
GM? | Alicia's Force 6 Fire Spirit -
Spirit Initiative:
2d6+15 22 [4, 3] | Came in at Pass 2, currently at Pass 3, so Initiative drops to 2
Out of Action Passes (Still allowed one Free Action minimum [more based on GM discretion] according to Page 160 of the Core Book of SR5)Jayde Moon | Betsy -
Some initiative Rolls 
:
1d6+9 14 [5] | Came in at Pass 2, currently at Pass 3, so Initiative drops to -6
Lusis | Luz (Using prerolled result, since I cannot find a new roll) - 8+1d6: 13 [1d6=5] | Two action passes have gone by, so Initiative drops to -7
saithor | Alicia -
Alicia Initiative:
9+1d6 10 [1] | Came in at Pass 2, currently at Pass 3, so Initiative drops to -10
Currently Outside of Combat. GM decision (because he's trying to fix the damn train before it crashes)adamu | Al - (Using prerolled result) 2d6 + 11 → [6,6,11] = (23) | Engaged in combat before everyone else, so is at a fresh roll (not currently engaged in combat, thus outside of Initiative)
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It should be noted the Wound Modifiers technically affect Initiative according to Page 160 of the Core Book.
Wound modifiers are applied directly to the character’s Initiative attribute. These changes are made immediately after the injury occurs and can affect the initiative order even within the same Initiative Pass.
This means that anyone with wound modifiers, such as the Spirit, may actually be out of Action Passes. I think the Spirit just took 6 boxes of damage, which is a -2 modifier, which would put the Spirit at 0 Initiative and thus out of passes.
Edit: Also, not sure if everyone has done their Action Pass 2 Actions, because schedule's can really interfere with the order of PbPs.