So what ships was the original idea here meant to be done with? The 18 base ships? But then why is this in the mods forum?
A modded ship? But the points system seems to benefit starting with
more on your ship, not less.
What behaviour are you trying to encourage in an UP ship challenge? Presumably, making a mod ship that seems very weak but manages to travel a long way. In which case I think the points ought to be based on the
starting ship configuration, plus perhaps some amount for each sector travelled. Something like: 50 points for no shields, 10 points for 1 shield bubble, 0 points for 2+ shield bubbles. 50 points for <2 weapon power, 30 points for <4 weapon power. -25 points for an offensive drone or a starting teleporter. -25 points for cloak. Reactor points: 100, minus 10 for each bar of power you start with. 20 points for <3 starting engines. And so on.
I imagine some of the Zerg ships in my sig ought to be worth a look for an UP ship challenge

Starting with neither shields nor cloak is very tough, although in the more general case I suppose starting with some OP weaponry could make up for it.