Had another look at it. Fired right up no problem, but it is doing "that thing" still.
-The alignment looks good.
-The dime shaped flame spreader was not quite parallel and the end of the tube there is rusty raggedy. I clumsily broke off the dime shaped deflector disk trying to bend it down a bit. This did not seem to make any difference to the flame after that thank goodness.
The adjustable air shutter at the orifice end is more like half open instead of 1/4 the way. Rusted in place.
So the thing it is doing-- It burns nicely for few seconds not much noise at the water heater end, then back at the orifice and air shutter holes, it starts making a loud "Tshhhh" hissing blow- torchy burbley sort of noise and an intermittent bit of flame comes out the air shutter holes (very little). The main flame keeps going at the water heater end, but seems disturbed (hard to describe)when this all happens.
The "event" stops after a few seconds and after some more seconds it starts again(longer time with no event than the time the event takes) The times it happens varies and how long the event lasts each time varies. This will continue until the water is hot and it all stops about 45 minutes later
That is why I thought there might be something in the gas valve "block thing" that was loose debris or whatever that I could clean out of there.