I installed the base sheet, then cut the plenum after that. Just be really careful about your Z. The last thing you want to do is cut through the base sheet and hit a steel cross member.
On the plenum, the channels only need to be 1/8" deep. Cutting deep channels into the base sheet only weakens the table. It does zero in regard to hold down or airflow.
Be sure to seal the plenum as air will leak through the sides of the base sheet if you don't do it well enough. I used four coats of heavy urethane floor finish to seal the plenum. It was nice and shiny when finished. Your spoil board should be well sealed on the edges as well. I suggest sealing the edges of the trupan sheet before gluing it to the plenum and be sure it is well sealed or you'll have a significant leak from that source.
A final suggestion would be to use 2" flex pvc instead of rigid pipe. It's about 100 times easier and requires almost no exact measurements or cutting. It attaches just like rigid pipe and is impervious to collapsing under vacuum. It is a bit more expensive but is well worth the effort. As a side benefit, the flex PCV will have a lot fewer (like zero) elbows so all turns will be gradual and cost very little in resistance in the flow.
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2013 PRS 96x60x12 (Centroid upgrade)
4hp Spindle
12" indexer
Aspire
Rhino
Fusion 360
Ferrari 360
Prusa MK3S+
Prusa XL multi-tool