If the engine shakes and knocks when using starting fluid, it means the engine is too warm. The starting fluid is igniting too soon and trying to make your engine turn backwards!
When you replaced the injection pump, did you remove the gear housing?
Sometimes these IDIs can take some time to bleed the air out of the injectors. If you are getting smoke, it sounds like you are getting fuel tho.
The engine has to spin fast enough to light these engines off, especially if the timing is off, which it probably is, since you haven't even started it yet.
I would abandon the glow controller and go to a manual system. At least bypass it until you get the engine running. The old 6.9 glow plug controller is just a bunch of burnt up glow plugs waiting to happen. If it hasn't already.
Check the wires supplying the power to the relay at the connector. Often these connectors will corrode/burn up and be a high resistance connection at high amps, like when you are trying to glow your plugs. You will still get 12 volts at the relay!
Oh, and you absolutely need power to the Fuel Shutoff Solenoid ( the big spade connector on the IP). Again, it sounds like you do because you are getting smoke.
I have had good success using starting fluid to start engines that I have done a lot of fuel system work on. I don't usually run into weather that is too hot.
Last week we had so much snow it broke 4 big branches off my Elm tree.
Granted that is unusual even for here.
Good luck getting it started!