It is probably originally negative earth but if fitted with an alternator to replace the original generator, it is now certainly negative earth - and incorrect polarity could cause the fire, although this would have happened as soon as the battery was connected, as the alternator would appear as a dead short.
Identifying wires by colour when the harness has certainly been modified is not very useful. Usually, a melted wire means that it has shorted somewhere, and if it did this when you tried to start, it may be the wire to the alternator which is supplied with power when you switched on the ignition, and this is either shorted or the alternator has developed a fault. On the other hand, it could be the main battery feed to the alternator, which rubbed through the last bit of insulation when the engine vibrated. Bit hard to tell without looking which terminal on the alternator it is connected to (and since the alternator is aftermarket, I have no idea which alternator it is).
I suggest a look at the wiring by someone with auto electrical knowledge would be worthwhile.
John
John
JDNSW
1986 110 County 3.9 diesel
1970 2a 109 2.25 petrol
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