Did the lamps work correctly before the ROM change? Can you try a different lamp board? Do they blink in test mode?

comparing what lamps are not working to the lamp driver schematic may give a clue as to if its a missing lamp signal. Like if lamps on connected to each decoder output 0-3 are stuck on or all the lamps not working are associated with one decoder chip. SCRs usually fail off, but sometimes fail always on, I guess its possible a bunch of bad SCRs but seems unlikely if its more than one or two stuck on.

Check the lamp address and lamp data connectors going from MPU J1 to the lamp board.

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3 ball game pops/spinners do not alternate.
5 ball game pops/spinners alternate

So on a 3 ball game, it's normal to have the pops and spinners always lit..... not the rest of the lamps though. Sounds like an issue.

Current version is 31

Audit #1 (Replay level 1)
Audit #2 (Replay Level 2)
Audit #3 (Replay level 3)
Audit #4 (HSTD)
Audit #5 (current credits)
Audit #6 (# of games played)
Audit #7 (# of replays)
Audit #8 (Low score to date)
Audit #9 (Coin chute 1)
Audit #10 (coin chute 2) *doesn't exist!!
Audit #11 (Coin chute 3)

additional audits

audit 12 - # of times HSTD beaten
audit 13 - # of times bonus max collected at saucer
audit 14 - # tilts (in game only)
audit 15 - # extra balls
audit 16 - # completed 1 player games
audit 17 - # completed 2 player games
audit 18 - # completed 3 player games
audit 19 - # completed 4 player games
audit 20 - # matches
audit 21 - # games abandoned (restarted before game over)
audit 22 - # free games paid
audit 23 - # left drains
audit 24 - # right drains
audit 25 - # SDTM drains
audit 26 - # specials
audit 27 - # slam tilts
audit 28 - tournament setting status (!0=tournament mode)

Tournament mode automatically disables any replay knocking
from specials/scores as well as blocking extra ball awards.

No, it's stock behavior.
Here's the bally code for it:
ldb $4E ;dips 9-16
bpl L170B ;dip 16 off, branch (3 balls per game)
sta 3,x ;light pops/spinners (A contains #$ff here, which blanks lamps)

Any 50 point score add (might be 10 point adds) runs the following as part of its code:
;swaps entire contents of lamp locations $203 with $204
ldx #$0200
lda 3,x
ldb 4,x
sta 4,x
stb 3,x

Since 3 balls per game sets all those lamps ON, it's swapping like for like, on for on. When set to 5 balls per game, some of those are set off.
They actually specifically turn all those lamps on at start, and only off if set to 5 balls per game. You could try it at 5 balls per game if you like and see if it works it should I've never actually tried mine that way.

Here's the changes between 27 and 31:

;6-25-2012
;v28 Revamp drop target handling; still all down with no where to go occasionally.
; Add in switch strip in main loop for c1r6 (LSTD flipper cabinet switch)

;v29 drop target handling revamp didn't work in v28, corrected in v29, tied to solenoid period timer

;11-2-2013
;v31 hold in left flipper button at boot to clear LSTD

Not a lot. Left flipper button switch is an added switch that you have to isolate from the high voltage flipper button.

$100 for an NOS PF was a great deal. I remember seeing one at pinfest several years ago from Mark Clayton (RIP) and it was pretty cheap but very yellowed. I should have bought it as NR is one of my favorite early solid states as well. Great party game, especially for dollars. Love giving a big shove to the game to save from an outlane, thinking I got away with it, ball comes into inlane and I realize I've tilted..... doh!!