Here's some input, based on my experience, I hope it's helpful:

Second Chance Flasher
906s belong in the Second Chance insert. 555 sockets look similar to 906s, but the 906s are a bit bigger - are you sure 906s don't fit? Flasher circuits operate at a higher voltage than controlled lamps, so only flasher bulbs (906, etc.) should be installed in flasher sockets.

Mini Playfield Flasher
Have you tried swapping out the bulb? Also make sure all the wires below the playfield are connected to the mini playfield. I've missed one or two from time to time and have had this happen to me. The Mini Playfield Flasher and Doctor 7 flasher bulbs are both driving by the same transistor (Q42), so it's probably not the problem. Most likely a bad bulb, connection, or wiring issue.

GI lighting
You can tell which "string" of GI bulbs are where (left, right, etc.) in the Operator Test menu, go through the GI tests and it'll illuminate (ha!) which are which.

Intermittent Controlled Lamps
The 555 sockets that "secure" to the lamp boards under the playfield wear out over time. The contacts get dirty, bent, etc. and that can prevent a good connection with the lamp, this is probably your issue. Remove the sockets for the lamp board, remove the bulb from the socket, clean the pins and bend them so they make better contact to the wires on the lamp base.

Fuse F109
F109 is for GI string #2. Also keep in mind that flashers are disabled when the coin door is open, this may have been why it was working during gameplay (coin door probably closed) and not in the test mode (coin door open).

The previous owner may have bypassed the coin door switch that disables coils and flashers, which is normal WPC behavior.

Freds13:
Go into the Test Menu, select General Illumination (Test #6), then step through all these tests, which will include tests of each individual GI string. This will show you which bulbs are connected to which string. I know of no standard bulb count for GI strings, depends on the game layout and total bulb load per GI circuit.

I could have sworn DW had the coin door switch, but upon further research, it looks like this was added during production of Twilight Zone, which was after DW.

It's not like Christmas lights where if one is out they are all out, they are wired in parallel. If one bulb is bad, it will be the only one that goes out, it doesn't take down the whole string. If a whole string is down, check for voltage at the sockets, then the connector, then the header to track down your problem - or find the blown fuse.

F109 probably blew again and you've got a short somewhere. You could try removing the connector from the header and measure the resistance of each GI string, to see if the one that's problematic is shorted or has less resistance than the others (which draws more current, blowing the fuse).

Common choices for connectors are the crimped pins (trifurcon) and a good quality molex connector. Great Plains Electronics sells lots of good products. You need the 0.156" pins and connectors.