Wow, that's a pretty weird line-up right there. I'm glad you had fun with it.
1) If two ships with the same Pilot Skill cross the finish line on the same turn would that be a tie or would it go to whoever had initiative?
The way I see it, the ships should get their final placements according to the order that they physically crossed the finish line. I see "Pilot Skill" as a timing mechanic, not a reflection of actual "pilot prowess" so it doesn't bother me if a PS1 ship wins the race during the same round that a PS4 ship crosses the finish line. For timing purposes, lower PS works in your favor in this race if you want to move first, but higher PS works in your favor if you want to maximize your combat potential.
2) Have you thought about allowing ships to buy upgrades they can't normally have (besides Elite Talents) with Credits earned? Maybe with a 10k credits per point cost of the upgrade since they will only be good for one race? Such as giving a Tie Fighter Advance Sensors for 30k... or an Ion Turret for 50k? Thus really allowing the racers to jury rig their ships for the single race.
There might be some overpowered interactions doing that, but I think it'd be fine to house-rule that. Try it out.




