It is like some areas are just not being extruded at all.

Because that is what is happening. Wood filament is just PLA mixed with wood particles suspended in it. These particles are very likely getting stuck in the printer nozzle and stopping any more filament from being extruded. This is not the only cause of under extrusion like this but the most likely.

Given it clears its self up it is probably that the blockages are clearing themselves eventually with enough time/pressure/heat behind it. Or it could be a particle moving around inside the head (which I think is less likely).

Best thing is probably to get a larger nozzle that will be less prone to being blocked by larger particles in the wood PLA. You can also clear the nozzle as well with a tiny needle or a cold pull of the filament. This may help for a bit it there is stuff built up inside the nozzle or if it the blockage is self clearing it may not help at all (but wont hurt anything). But the better solution is likely a larger nozzle.

Looks like classic wood filled filament clog. You see standard plastic is like water flows well this has sawdust mixed in so it's more like peanut butter. Check for overheating it is probably turning into charcoal and sticking or the nozzle is 0.4mm so it's clumping and if you are in humid environment it could just be absorbing moisture that could be it too.

I would try with 0.6mm check if it feels moists try with ironing off and see it is running too hot to make it like this.

The rest of the print is perfectly fine but the top layer is having issues? I would check the settings that effect only the top or top / bottom layers.

You said it's a new filament, is it a new profile for the new filament as well or have you successfully printed other filaments with the exact same settings?