Sounds like you have a bit of a problem, but it should be possible to nut it out if you go at it logically - I find in these circumstances that labelling each wire as you figure out what it does is worthwhile. (a couple of inches of masking tape and a biro)
The "relay" attached to the alternator is probably an external regulator - mine has that.
Re your lights - problems with these are often earths. Check where the lights are actually earthed, and that they really are earthed. Mine were earthed to the radiator support panel - but it was not electrically connected to the chassis! Fixed that with a earth strap directly from the negative of the battery to the panel.
Most Landrovers of that vintage have been converted to negative earth because they have had alternators installed and/or to run negative earth electronic equipment.
John
John
JDNSW
1986 110 County 3.9 diesel
1970 2a 109 2.25 petrol
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