I don't know if you have Clay's guides for pinball repair, but I copied/pasted the relevant section from his Data East repair guide here...plenty of stuff to check!
If the Flipper(s) Don't Work at All or are Intermittent...
Solid state Flipper games (Robocop and later):
On games with electronic flippers, clean the EOS switches (if the game has them) and the cabinet switches with a cotton swab and alcohol. This is especially the case if the flippers are intermittent, working only sometimes, or sometimes weak flippers. This only takes a second to do and can solve many problems.
Check the flipper fuses. For solid state flippers (Robocop and later), the fuses are on the solid state flipper board, which is on the side of the cabinet under the playfield. The flipper will also not work if the 50 volt fuse on the PPB board is blown (this fuse is located at the top center of the PPB board, to the right of the four inline fuses at the top left).
Check the fuse clips on the solid state flipper board. Often these fatigue or break and will not grip the fuses. Push down on the fuses as installed in the flipper board. If the fuse clip "Y"-out, the clip is bad and must be replaced.
Look for damage on the solid state flipper boards. Since these boards are located below the playfield on the left side of the cabinet wall, they are very easily damaged. A common problem is a broken or open TIP36 or TIP42 transistor on the solid state flipper board. The position of the board(s) under the playfield (on the side of the cabinet), permits easy damage if the playfield tilts and falls inside the cabinet (this especially happens on Ninja Turtles and later games with playfield mounting slide rails). If the playfield falls off the slide rails and into the cabinet, it can easily tear components off the solid state flipper boards. Several transistors with heat sinks stick out the furthest from the board, making them easiest to damage.
Check the LEDs on the flipper board. The LEDs indicate that the flipper cabinet buttons are being pressed. There is one LED for each flipper in the game. If pressing the flipper buttons does not flash the flipper board LED(s), try cleaning the cabinet switch and flipper coil EOS switch (if the game has them) with alcohol and a rag.
On Jurassic Park, Last Action Hero, and Tales from the Crypt, check the normally closed EOS switch. If the EOS switch is dirty, or has a wire or switch blade broken, or is mis-adjusted so the switch is not closed when the flipper is at rest, the flipper will not work! Test by using an alligator jumper wire across the EOS switch. This problem only happens on games with solid state flipper boards #520-5033-03 and 520-5070-00 (which is replacable with #520-5076-00 and #520-5080-00 respectively, which fixes this problem). These flipper boards can also be modified to act correctly, like the later flipper boards. See the DataEast service bulletin number 54 by clicking here, here, and here.
Check for voltage at the flipper coil (on games WWF and later, make sure the coin door is closed!) With the flippers enabled (in game mode), use the DC voltage setting on the DMM. Put the black lead on ground (grounding strap inside the coin door). Put the red lead on the flipper coil lug connected to the BANDED side of the diode. Press and hold the cabinet flipper button (no voltage will be shown until the cabinet button is pressed). The DMM should show a spike of high voltage, which settles down to about 7 volts DC. No voltage means a fuse is blown, or there is damage to the solid state flipper board, or the flipper enable relay. Repeat this step in attract (game over) mode. But this time put the red lead on either flipper coil lug. With the flipper cabinet button pressed and held, look for a voltage spike which settles down to about 7 volts DC.
If there is no power to a flipper, and the solidstate flipper board fuses are good, next test the TIP36 transistors on the flipper board (should get .5 to .7 volts using the DMM diode test). Even if they do not appear to be damaged, this is a common part to fail. If a TIP36 fails, its associated flipper will not function at all. See Checking/Fixing Transistors and Coils for procedures on testing transistors.
Both flippers work fine, then especially when holding them up for a few seconds, they die. They start working again a few seconds later. Sometimes the flippers may only get the high voltage power side, and will blow the low and/or high power fuses when used. Check all diodes and transistors on the Solid State Flipper Board (.5 to .7 volt range on the diode DMM test). If all seem fine, this can often be attributed to the 4093 chips on the solidstate flipper board (replace both of them and use sockets).