When you say you verified valve timing, was that with the camshaft locking plate inserted and the rear cam gear removed?
This sounds like textbook incorrect pump timing so I think you are correct about that. The good news is that it will be easy to fix -- you just need to get the right equipment and process. Very simple steps compared to the other major work you have already successfully done.
I would guess one of these two things has happened.
1) Pump is timed 180 degrees out from camshaft. Did you verify that the cam lobes for #1 cylinder are both pointing upward (#1 compression TDC) when the injection pump gear's timing is approaching the notch on the injection pump bracket? The engine will still run with timing 180 out but extremely poorly.
2) Timing is not 180 degrees out of phase, but is also not set correctly. See below.
The way you get the marks to match better is with the timing process using special tools -- BUT at the same time, the marks don't really matter. They only are an extremely rough guide help you confirm that you are timing the pump to the correct cylinder, lining up to TDC. From there everything is done with fine adjustments using a dial indicator as shown in the factory service manual (or find youtube videos online like this one
https://www.youtube.com/watch?v=LWyhxPM9TOE). Did you use that process?
It's not adjusted tooth by tooth -- that is much too large of an increment to achieve the needed precision.
A whole tooth???? Oh yeah, it sure could.
Timing is required to be EXTREMELY exact on this engine, like on any diesel without computer control. Even a fraction of a tooth out of time will make it start/run poorly, and on many engines, a full tooth off will either make it not able to start (if retarded) or risk blowing headgasket or bending connecting rods (if advanced). This is why the timing on this engine is all done with taper or friction fit, no keyways, and why the timing process and tools are so sensitive. You can't just "line up the marks and go" like on a gas engine or computerized diesel. Visual timing just doesn't work here, you *have* to use the correct locking tool for cam timing and the dial indicator for pump timing, and go through the steps in exactly the right method and order.
The good news, again, is that as long as you have the necessary equipment and info, the process is easy and the engine will run perfectly afterwards.