Is a Common Soul gem with an Ancestoral ghost supposed to pay out 4000 gold???

Because... I could be making thousands of gold, for the purchase of one common soul gem, 40... with a 1 shot kill.. at level 3 on a summoned anscestoral Ghost..

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Is that Vanilla Morrowind or a mod I am using altering the pay out?

Yep. Harvesting souls is a very lucrative job in morrowind.

If you are worried you get too rich using this, you could try http://www.nexusmods.com/morrowind/mods/19510/?'s fix for it. Check 'Soulgem value rebalance' under Game Mechanics Change.