Yes there should be no obstruction so the cell can detect light, if there was the burner would ignite then go to lock out due to no flame sensing.
I mentioned the pump gear set, drive key and coupling but did not say have a look yourself lol. I know you have a back ground in engineering but I only ever opened up a pump if I had spare seals and pump at hand and after I was confident there was a problem with it. What was the drive key and pump coupling like? These pumps should all be put back together with a certain torque as we discussed above.
I mentioned the pump gear set, drive key and coupling but did not say have a look yourself lol. I know you have a back ground in engineering but I only ever opened up a pump if I had spare seals and pump at hand and after I was confident there was a problem with it. What was the drive key and pump coupling like? These pumps should all be put back together with a certain torque as we discussed above.