Couple things..

With any of these games there's some DIP switch settings that will control max credits, display of credits, match features, etc. There's then also high score levels and bookkeeping values stored in the 5101 RAM that needs to be zero'd out -- you get to those via the self-test switch (see below).

Here's the manual:
http://mirror2.ipdb.org/files/887/Stern_1980_Flight_2000_Manual.pdf

Take a look at Page 10 for the DIP switch settings.

Page 6 will then have the self-test & bookkeeping functions listed.

The first five times you hit the button will be self-tests, number of the test will be on the credit display.
01 - Burn-in test, all outputs tested
02 - Lamp test, all feature lamps turned on and off
03 - Display test
04 - Solenoid test
05 - Switch test

Hitting self-test again, you should see 01 on the credit display. That's the start of the bookkeeping.. 01, 02, 03 are high score thresholds you can set... the remaining of the bookkeeping functions are things that the game keeps track of (number of coins, replays, etc). You'll need to zero each bookkeeping value out first by hitting momentary button at the top right of the MPU board. For the high score levels (01, 02, 03) you can use the credit button (game start) to set the high score level. Everything else just gets zero'd out. Press the self-test button to advance to the next bookkeeping value, zero-out, self-test to advance, zero out, etc. After bookkeeping function 18 it'll restart the MPU.

Try zero'ing out the bookkeeping and setting some of the DIP switch settings mentioned in the manual. It looks like the game is booting and just not showing a high score? Does it start a game if you press the start button with the correct number of balls in the ball trough?

Hopefully that gets you further along..

Ah, whoops... you're right it tops out at 18. I just looked at the manual's bookkeeping functions & it mentions "test switch push number" 23 is bookkeeping function 18.

Is the 20 showing up on the 4th player display? Can you start a game now?

The number in the right of the credit display is the match number. It's been a while since I've worked with an MPU-200 machine, but that match number probably reflects the last match number given. Or it may be random each start-up. I'm a bit rusty on the expected behavior since it's been a few years since I've had a F2K or MPU-200 machine setup other than a Black Beauty Shuffle Alley.

Coils in the multi-ball loop should activate at some point to kick any balls out, I'm not sure if activating on start-up is expected.. but I think it activates those 3 times to kick the 3 balls out that could possibly be there. Someone else would need to confirm that though.

Are the 06 credits showing not what was there when the game last was turned off? That number should reflect the last number of credits that were on the machine. So if you add a 2x more credits via coin switches it should show 08 any time the game is started up until you start playing some games on the machine.

As far as starting a game, are all the balls in the ball trough? Some games need to recognize all the balls via the ball trough switches before they'll allow you to start a game. It looked like your board got hit a bit by battery leakage -- is there any discoloration over by the J3 header on the MPU (cabinet switches)? You may want to try wiggling that connector slightly and then pressing the credit/start button (again, with all the balls in the ball trough).

Was referring to this pic: https://pinside.com/pinball/forum/topic/feedback-on-flight-2000-repair-and-if-i-should-purchase/page/2#post-3633445 -- I just noticed some discoloration in the ground trace at the bottom of the board & some green/blue at one of the battery through-holes. It doesn't look too bad though.

You'll probably want to go into switch test (via self-test button) and try each of the ball trough switches independently to make sure they're being registered. And also try the credit switch that way too.