WARNING: POST MIDNIGHT RAMBLINGS OF A SEMI-EDUCATED FOOL:Unless with your mods you're using a later loom after the point at which Mr Toyota swapped to negative switching, in which case whoever helped you with any wiring modifications may not have got everything quite right eg, from memory, a friends FJ73 was negative switched and we found out the hard way
Sample of Toyota negative switching from the mid to late 1980's attached. If the add on loom is using the factory switch/stalk to trigger the ground for the relay, it could be hindering the current path to the high beam indicator which from factory is somewhat counter-intuitively fed through the low beam headlight element (NB, i think this diagram might've been USA spec so LH/RH may be switched depending on which side the loom ran)
This diagram is a bit counter-intuitive, in that it appears the high beam indicator is in fact connected to the low beam through the low beam element! When low beam is on, that side of the low beam element is grounded, so the low beam headlight element is on but the high beam indicator has 0 potential and does not glow. When high beam is engaged, both side of the the low beam element is now ~12V as the ground path is removed, which results in ~12v at the wire to the high beam indicator!
What's difficult to wrap your head around is this: if the add on loom has a relay coil negatively switched in place of the original headlight element, you would expect the high beam indicator to function as intended, as the coil of the relay would function similarly to the headlight element
... unless the coil of the relay has a much higher resistance than the headlight element, which makes total sense as the relay draws much less power!
If this rambling is correct, you'll find that the voltage drop across the relay coil and high beam indicator is analogous to resistors in series; the voltage drop is directly proportional to the resistance; the globe is only getting a fraction of the potential so will either glow very dimly or not at all. This could be easily confirmed with a multimeter; you'll find only a small voltage is present at the high beam indicator globe (installed), and nothing when headlights are off. You may even find that if you inspect in complete darkness the high beam indicator is glowing very faintly.
If this is the case, the solution would be to re-wire the high beam indicator; find where it T's into the old wiring, disconnect it and reconnect it to the high beam wire on the headlight plug on the new loom (assuming it is now positively switched by the new relay).