Here's my Wonder Boy repair log - some of the colour related faults, etc may help you to fix your board.
Note: there are two common types of original Sega Wonder Boy boards - one is a single board, the other is also a single but with a couple of daughterboards.
Symptom: Sega Ninja board, same hardware as single board Wonder Boy! -shimmering dots in sprites, also on the water level the normal horizontal lines have short vertical lines at each end, plus on one of the next levels the building roofs have similar vertical lines at the ends
Cure: Had to tie a 180 ohm pull-down resistor to pin 12 of the LS132 at location IC86 (replacing the chip and the capacitor (330pf, marked as 331) connected to some pins on that same chip didn't help)
Symptom: Horizontal lines through all sprites
Cure: Stuck outputs on pins 4 and 7 of the LS157 at location IC58 (original Sega single board)
Symptom: All background tiles, text and graphics data (but not the sprites) is scrunched up very tightly and corrupted in the horizontal plane (original Sega single board)
Cure: Dead outputs on the LS157 at location IC93
Symptom: No background being drawn except for a few random blocks (original Sega single board)
Cure: Bad outputs on the LS157 at location IC72
Symptom: The whole display is scrolling vertically, some graphics and text visible, game won't play (original Sega single board)
Cure: Bad outputs on the LS669 at location IC79
Symptom: Display is just a scrolling herringbone pattern (original Sega single board)
Cure: Bad socket for PROM PR-5317 at location IC7
Symptom: Assorted missing sync signals (original Sega single board)
Cure: All outputs bad on the LS164 at location IC31
Symptom: No colour video output, only video sync. Game plays blind. (original Sega single board)
Diagnosis and Cure: No clock inputs on pin 9 to the LS175's at locations IC107, IC108 and the LS174's at locations IC74 and IC74. This clock comes from pin 11 of the LS132 at location IC87, but the inputs to that were good AND replacing the chip didn't help. Then noticed that the capacitor at location C123 (just below IC87) had a 0.1uf cap in place – replacing that cap with a 220pf cap fixed the fault. Only knew that this was a 220pf cap from referring to a known good board, which had the cap code of '221'. Note: Removing the cap brought back the video.
Symptom: Using the Fluke, test main or sprite RAM – there's a R/W Error at the starting address BTS 40 (original Sega single board)
Cure: Bad LS245 at location IC125
Symptom: Two characters on the title screen are incomplete and partly 'smeared' (original Sega single board)
Cure: Broken track between pins 19 of the 27128 EPROMs at locations IC104 and IC105, so there was no connection to pin 3 of the LS273 at location IC99
Symptom: No background tiles, only sprites and a few bits of rubbish (original Sega single board)
Cure: Bad LS157 at location IC71
Symptom: Variable "phut phut phut" sound from the speak which is of the same volume irrespective of the pot setting, no other sounds
Cure: Bad LS4460N amp
Symptom: Sprites badly positioned and flickering on and off, plus badly broken up (original Sega single board)
Cure: The four LS157's at location IC52, IC53, IC57 and IC58 all had faulty outputs
Symptom: Screen is showing assorted short-ish, flickering horizontal lines. Also, the bottom quarter of the display is displayed four times, filling the screen (original Sega single board)
Cure: Bad outputs on the LS157 at location IC71
Symptom: Some of the colour shades missing, especially red (original Sega single board)
Cure: Some dodgy outputs on the LS175 at location IC108
Symptom: No video sync (original Sega single board)
Cure: bad output on pin 11 of the LS86 at location IC10
Symptom: Vertical scrolling is very jerky, bottom half of screen reproduced at the top during gameplay – no clock on pin 11 of the LS374 at location IC03 (original Sega single board) – a similar fault can also be caused by this actual LS374 being at fault (pin 8 being cut for example), shown as the lower part of the screen being too high (Wonder Boy sprite half hidden behind it) and when the ground angles upwards it's also drawn too high – in this case caused by the output on pin 6 being stuck High
Cure: Bad output on pin 12 of the LS157 at location IC71
Symptom: Vertical scrolling not working (original Sega single board)
Cure: Bad outputs on the LS273 at location IC03
Symptom: Some colours wrong (original Sega single board)
Cure: Bad LS153 at location IC9
Symptom: No sprites (original Sega single board)
Cure: Bad LS244's at locations IC2 and IC3
Symptom: Display split in half horizontally, just the two right halves doubled up (original Sega single board)
Cure: Bad LS283 at location IC40
Symptom: On power up, 'WONDER BOY' text split horizontally and high scores too spread out (original Sega single board)
Cure: Bad LS283 at location IC50
Symptom: Text, graphics, etc all consists of short, thick, vertical lines (original Sega single board)
Cure: Bad LS283 at location IC01
Symptom: Only the base of the screen is drawn, multiple times (original Sega single board)
Cure: Bad LS157 at location IC72
Symptom: All text and graphics repeated vertically eight times (original Sega single board)
Cure: Bad LS157 at location IC83
Symptom: Sprites displaying incorrectly (original Sega board with daughterboards)
Cure: Output pins 5 and 6 not toggling on LS74 on the Sprites daughterboard, bad outputs as inputs good
Symptom: Colours wrong (original Sega board with daughterboards)
Cure: Combination of a bad 6116 RAM chip at location IC151 and a bad LS175 at location IC152
Symptom: No sound (original Sega board with daughterboards)
Cure: Combination of a bad 6116 RAM chip at location IC7 and a bad LA4460 sound amp, both replaced and sound working fine
Symptom: Background partly garbled, no black areas where they should be at the top of the screen and other faults (original Sega board with daughterboards)
Cure: Bad 6116 RAM at location IC102 - replaced
Symptom: The ground is broken up, looks like there's been an earthquake, some segments a bit higher than others, the layout of the broken segments varies from game to game. Also occasional thick vertical black bars above the ground are, plus some background graphics corruption, such as random bits of other graphics in the totem poles in the third section of the first level (original Sega board with daughterboards)
Cure: One poorly seated chip in program EPROM sockets 1 – 6 but not sure which one!
Symptom: Vertical scrolling and positioning messed up, for example on the title screen the red WONDER BOY text scrolls up very jerkily and ends up too high (positioned behind Wonder Boy and his girl) plus that same text is split horizontally down the middle with a large gap between the two halves. Also affected by this fault is the vertical scrolling of the high scores which is also jerky and mis-placed. Finally, the in-game ground graphics are duplicated vertically so obscuring the main character, etc. (original Sega board with daughterboards)
Cure: Bad 74LS283 at location IC6 on the 834-5541 daughterboard (Additional: had a similar problem occur a few hours after fixing this one which turned out to be the other LS283 (location IC7) on the same daughterboard – in this case though the scrolling was less jerky and the Wonder Boy text only ended up a little higher than it should have been)
Symptom: All graphics, including text, cut in half and roughly doubled horizontally (original Sega board with daughterboards)
Diagnosis: Found that grounding pin 3 of the LS368 at location 1U caused the problem to be resolved. Replaced the 368 but fault remained. Traced pin 3 (an output) to the LS283 at location 1S, piggy-backed a good LS283 on the existing one and the fault went away.
Cure: Replaced LS283 at location 1S
Symptom: All sprites are a thin vertical line, or not visible at all (original Sega board with daughterboards)
Cure: Bad outputs on the LS175 at location IC91, particularly pin 3
Symptom: Thin horizontal lines through all sprites. Also some of the background. Plus thin vertical lines on the left half of the display (original Sega board with daughterboards)
Cure: Bad output on pin 6 of the HC32 at location IC11
Symptom: Most colours non-existent, all that's displayed are shades of a yellowy-green and an off white for the text (original Sega board with daughterboards)
Cure: Bad LS245 at location IC150
Symptom: Screen display doubled vertically (original Sega board with daughterboards)
Cure: Bad output on pin 9 of the LS157 at location IC2 on the 834-5541 daughterboard
Symptom: Screen display doubled horizontally (original Sega board with daughterboards)
Cure: Bad output on all relevant pins of the LS157 at location IC1 on the 834-5541 daughterboard
Symptom: No blue (original Sega board with daughterboards)
Cure: Pin 11 of the LS175 at location IC152 was stuck high internally and no output from pin 10 – replaced IC
Symptom: Vertical scrolling not working at all, loads of short horizontal dashes flickering all over the display AND the dashes were additionally being drawn in the overscan areas. (original Sega board with daughterboards)
Cure: Bad LS245 at location IC5 on the 834-5541 daughterboard
Symptom: Sprites problem – for example, on the title screen with Wonder Boy and Tina, Tina is a smeared, horizontally stretched mass of pixels, and some in-game sprites are similarly smeared. (original Sega board with daughterboards)
Cure: Bad LS245 at location IC108 – replaced