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On my MY Sedan when I did the EJ conversion I had two positives going to the alternator, an 'always on' and an 'ignition'. I hooked them up to the EJ alternator in what I thought was the right order, but I think I got them backwards as it would drain the battery over time and if I put my head right up to it there was a slight whine coming from it even when engine was off.

The EJ Alternator has two connections for +ve power, should I have ig in one, and constant in the other ? If so I'm guessing I just swap over what I've got as I probably got them wrong. Otherwise maybe I should unhook the constant all together ?

There are a few different EJ alternators but from your description it sounds like you have a gen 2 type. The large white wire is the sensing wire, it just goes to the battery(just connect it straight to the post on the alternator). The other wire(black/white) is the charge light wire. There is no ignition sw wire on these alternators. The charge light must be working for the alternator to charge correctly. The black/white wire on the MY will be ignition power so don't just assume that the colours will match.
If you have a lot of high current electrical equipment you should run some new wires from the alternator post to the battery via a fusible link as the orignal wiring is not large enough for the alternators output. This is only usually and issue if you have large spotlights or run fridges etc.

I recently replaced an alternator on my 92 Liberty. The original plug & socket had 4 terminals, then replacement one has only 3. Works fine & dashlight works. Apparently the extra one isn't needed?

Early alternators have a 4 pin round plug, they require sensing wire, light and an ignition feed to charge, the 4th wire is for Jap cars for some kind of ecu control.
2 Plug ecus are much more reliable and charge higher at idle. It is a simple job to replace an early alt with a 2 pin gen 2 alt(bolt on and minor wiring change) This is a good upgrade.