Most likely a bad ground. Many 40 owners have run a dedicated ground wire from the signals to a good body/chasis ground.
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Be aware that the flasher is a CURRENT driven device. That means that it MUST have at least 1.3 amps of current flowing through it BEFORE it will flash. What this means to the end user is that at least TWO bulbs must be lit before there is enough current to cause the flasher to flash. That is why the Hazards almost always work as it turns on all four bulbs. The turn signal only flashes two bulbs.
So...
If your battery is low (below 12.5 volts)
Your harness has bad grounds at the lights (high resistance)
Your bulb sockets are corroded (high resistance)
Your bulbs are the wrong type (not enough current flow)
Your turn signal switch is dirty (high resistance)
Your connections between any of these are dirty (high resistance)
Your flasher relay is defective (very possible if OEM) CityRacer sells an NEW OEM replacement or you can order one of my LED flasher kits (you do not have to use LED bulbs if you don't want to. It will flash normal bulbs also)
Your flasher relay works but has dirty relay contacts (high resistance)
If any, all, or some of the above apply...Your turn signals will NOT flash!
These high resistances add up quickly. If there were no resistances in the turn signal circuit you would have battery voltage (+12.7 volts) AT THE LIGHTS! The voltage readings posted above show a lot of resistance in the circuit. Just think about the path the current must take to reach the rear turn bulb. The key switch contacts, the fuse block fuse contacts, the turn/hazard switch contacts, the flasher contacts and all the bullet connectors and wire it must pass through, then finally the bulb sockets contacts, and last the ground connection. If you would clean everyone of these areas properly, you should see that voltage go up.
Another thing about voltage: Incandescent bulbs are rated at battery voltage for their rated lumen output. The lower the voltage at the bulb, the dimmer the light. A bulb rated at 13.2 volts will be how much dimmer at 10 volts? This is why the headlight relay harnesses were invented: to get the voltage at the head lights as high as possible for the brightest lights.
OEM colors for turn signals
Green = Park
Green/Orange (early) or Green/Black (later) = LEFT Turn
Green/Yellow = Right Turn
Green/Blue = Turn switch to flasher (L) to bulbs
Green/White or Green/Red Flasher (B) +12V
Just my experience. If the top was on properly before and nothing else significantly changed, then I would loosen everything back up including the window frame two dash knobs and go from there. If the body was off then losen the body mount bolts. The two dash knobs have a spacer to limit them and the dash may come into play as well.
How does the door striker line up? If the door is correct, then the top is off.
To my knowledge, the previous owner never had the top on, and I think he got the vehicle in pieces when he bought it. At some time, I believe the rear sill was replaced, and possibly the rocker panels, but I'm not certain.
Before we started making adjustments, the door striker was shimmed about 1/4". The door had been rubbing the rocker, but the new hinges helped alleviate that a little.
We did loosen the window frame, but when I tighten everything, it draws the wind frame towards the driver and towards the door, making the problem worse if that makes sense.
Doesnt the part that runs above the door to the winshield frame have a little adjustment? Its been a while, but I recall it being two parts and I think some of the holes are elongated.....but I could be wrong.