I think NE Ray does less damage than comparable spells because it can also be used to heal undead. And it allows a saving throw because most negative energy effects allow a saving throw. Both limitations seem reasonable but combining them in one spell makes for a weaker spell when compared to other 1st level spells. So I've re-thought my original level increase.
I'd keep the slower increasing damage but drop the saving throw so it would match other 3.5 ray spells. Damage is damage whether its fire, cold, acid, or negative energy. The source of the damage only matters for creatures which are particularly resistant or vulnerable to that source. And since this particular source also heals undead thats why I think the slower damage increase is balanced.
With that in mind, NE Burst should definitely be only a second level. It does horrible damage compared to ANY other 3rd level spell (especially the most comparable 20' burst 3rd level spell!). In fact it does less damage than most 1st level spells, but it's much larger area of effect justifies making it 2nd level.
Finally, I'm thinking NE Wave is probably just right for the effect it has.