+2 funding per the official "oops" rule.
Pretty much this. But, at the end of the day, it's your game and you can play how you want.
As far as balance, the +2 funding is probably the best way.
I wouldn't mess with the upgrades at all. They're pretty powerful and you can make things quite easy. On my play through, we lost 3 in a row during March and April. That's 6 upgrades in a month and a half. By the 4th game though, we had it way easier due to those upgrades. We haven't opened box 8, but I'm betting
Spoiler (click to reveal)
it would be VERY BAD. That's 8 upgrades in 2 months. Big advantage for the players.
The other thing you could try is give yourself a bit extra on the win bonus if it's not adding something permanent.