Dan - I sympathise ...it is fiddly until you have done a few and suss out what works best for you.
To make sure you have the L or R pawl, just a case of holding it up and comparing to the one in there already - you need to make sure that when it pulls in the little arm moves the correct way to open/close the EOS switch.
I usually insert the flipper into the pawl, then tighten it just enough that you can still just twist the flipper around/move it up and down. At this stage get the height correct. Then as you say you want the plunger fully out against the rubber, get the flipper lined up ...if you have the pawl tight enough the flipper wont move on its own but you should be able to swivel it, if it does move on its own you need it a bit tighter ......
Once its in correct position I usually hold it with one hand and tighten the nut/or allen (depending which is easier to access) with the other. You only need a bit of a turn to secure. Now at this point the pawl will be holding the flipper pretty firmly so you can move the plunger where you want to allow best access to nut/allen and then REALLY tighten. As Andy said above. But not so tight that the pawl jaws meet !!!
With Bally Williams games there is usually a little hole on the playfield near the flipper, you can put a cocktail stick in this and rest flipper against it or even put the stick between the rubber and the flipper to hold it in position.
Hope this helps. Reading it back I'm getting confused

Would be easier if you were here and I could show you of course.
Chiz