Definitely don't want to use ether ever in these engines. Not even just a whiff of it. ESPECIALLY if the glow plugs are lit!!! I have a collection of shattered glow plugs on my shelf from people doing this on these engines and others like them (Ford IDIs, GMs, etc). Can also crack pistons, bend rods, bend or fracture crankshaft, blow head gasket, etc. It's the fastest and most effective way out there to turn a good engine into scrap metal!!
Same as a 6.2 or 6.5. These engines really, REALLY do not like ether. And there is no situation where ether will ever help. If the engine won't start and run on diesel, then it's not going to run on ether, as you already found out. So you get all the damage from ether and no benefit. These engines are extremely easy starting diesels when they are working right, and they are also extremely simple engines and easy to fix. If it won't start, you'll be able to figure out why without too much trouble.
Just some advice to avoid doing anything you will later regret.
You want to keep the ether far away from this engine at all times, no matter how tempting it might be. I will repeat, it can never help, only harm.
Timing 180 degrees out sounds like a possibility, though if that is true then it wouldn't have "run when parked". You say it smokes when cranking to start: does it smoke a lot? If so then you definitely have fuel flowing, but if not, then fuel injector prime is a question you could check by cracking lines open at the injectors.
Also, when you say timing marks are lined up, are you talking only about the mark on the injection pump lining up with the mark on the pump mounting bracket? What about the mark on the edge of the IP drive pulley? There is a notch on the pulley flange that should line up roughly with the IP timing mark with engine at #1 TDC.
If it definitely ran when parked, then timing being off is not too likely, but I would still rough-check it with the above method. That will not tell you if the exact setting is right but will at least tell you if it jumped a tooth.
If it ran when parked but doesn't start now, one more possibility is loss of ring seal from dry or stuck rings. This is very rare but we have seen it on engines now and then after sitting a long time. Solution is to do a compression test and/or add a little lightweight motor oil or ATF to the cylinders with injectors removed, then crank with injectors out to blow excess oil away and prevent hydrolock, then reinstall injectors and attempt starting again with the cylinders wet. If the issue is compression loss at the rings, this usually brings the engine instantly back to life.