WTG, Will
VERY detailed project you have on the go here. I'm looking forward to following along and learning some stuff I didn't know before.
For the lettering on the side as you said, PE is the obvious route. AFIK there are p/e letters available in eg 1/35 armor stores and shipbuilding stores - maybe you could use these?
As for logos etc., I would have thought that a scaled-down logo printed in card, cut out by hand or plotter and glued onto the resin master would perhaps give enough height for it to be visible on the resin casts? Just thinking out loud here...