The bolt holes in the valve cover will be bent down from past tightening, it's just thin steel, so when re-tightening they don't provide as much pressure between the holes as when new.
I would recommend straightening them, doesn't take much, but can make a world of difference.
Put something flat under the valve cover lip and tap it straight
Spreaders are OK, but if valve cover is bent it won't help.
Don't over tighten the bolts, it deforms the metal between the bolts, as said this is not a "pressure" area seal, it's just gravity pulling on the oil so a soft snug seal is fine.
The head surface the gasket seals will be straight, just make sure it is clean, run your finger over the surface to make sure, but this is a ground casting surface so stays pretty straight.
You can put a light on the exhaust manifold side and put a straight edge on valve cover seat surface to make sure there is no "dip" or deformity.
The valve cover side won't be straight, even after tapping it straight, I put sealant on the valve cover then place the gasket on it, then install it.
If the intake manifold overlaps under the valve cover you can put a dab of sealant where head and manifold surfaces meet, but just a dab.
Not sure for the 2.9l but you can get aluminum valve covers that don't bend, and look nicer