Nice, sounds indeed like you are on the right track.
These engines can be funny about starting with a couple cylinders down. I think it may depend on which particular cylinders are dead. In your case 1 and 3 are also positions 1 and 3 in the firing order. The engine may not be able to keep enough crankshaft momentum going with one cylinder (#5) trying to hit in between those two dead misses. And it only has three consecutive cylinders that can fire, so that's only half the engine (6,2,4). This is speculation but I think it might have a better chance of starting if it was two consecutive cylinders that were dead, e.g. 1 and 5, so that the rest of the engine could run on 4 in a row. But even then that would probably depend on other variables also, like ambient temp, compression on the other 4, pump timing, starter and battery and injector condition, etc. And of course the glow plugs on the 4 that have compression.
Anyway that's a long way of saying no, it would not be that surprising if two low cylinders prevented it from running, considering those factors above. One dead hole doesn't matter much but two or more somehow suddenly matters a lot more than one might expect. It's a fairly familiar fact to many of us here that starting these engines, assuming all else is in good shape, works like this:
6 glow plugs working: starts instantly, effortlessly, cleanly
5 glow plugs working: starts easily but rough and smoky until the one dead cylinder starts hitting
4 glow plugs working: can become very hard to start, sometimes impossible depending on other engine/environmental factors and perhaps on where in the firing order the dead cyls are
3 glow plugs working: engine almost always is impossible to start except by dragging the car (with standard trans), unless ambient temp is very warm and engine is in exceptional condition otherwise
Adjust those valves and see what happens! A seat of the pants leakdown test is always good info in this situation too. Dismantle compression tester, build air line adapters as needed apply shop compressed air to suspect cylinders (with the cylinder being tested at tdc with valves closed), and listen/feel for where most of the air is escaping: intake manifold, exhaust tailpipe, crankcase, or coolant recovery bottle. You don't need a leak down gauge to tell you fundamentally where your issue is coming from.
Then you can adjust valves and observe the difference, if the leakage was found in inlet or exhaust areas.