Chani you've received great input so far, all of it spot on. Hopefully things will be more opened up by June (we've just gone into our third big lockdown). For sure masks will be required everywhere public (whether people wear them, another story). Some additional thoughts:
Since you arrive on Sunday, your food choices may be limited. Buoy is open though, beer and food (awesome plexiglass floor to see the sea lions). The Columbia Maritime museum is well done (currently has a capacity limit) - fun fact, my dad served in the Coast Guard on the Columbia lightship docked at the museum. I'd head out to Fort Stevens State Park for a walk on the beach and to see the wreck of the Peter Iredale. Astoria Column does have great views but it's a very narrow climb (not for claustrophobic).
On the way to Depoe Bay
I also love the three capes drive, but the Cape Meares segment is closed due to landslide. I'd personally drive on through Tillamook (visit the creamery, cheese, ice cream, etc. is good any time of day). Then cut over on Highway 131 to Cape Lookout (great hike out and back) and then on to Pacific City. Late lunch at Pelican Brewery. If you're lucky you can watch the dory boats land on the beach. If you can get in, Tidal Raves in Depoe Bay has excellent food.
Depoe Bay to Silverton
You might consider back tracking to drive via Highway 20/22 to Salem on to Silverton, instead of going through Newport. I like the aquarium but given your time I'd skip it. The wineries near Silverton aren't that fantastic IMHO, so I'd suggest instead hitting a couple wineries on your way from the coast to Silverton. If you drive Newport/Corvallis route, take highway 99 and try Airlie or Emerson. If you drive Lincoln City/Salem route, take a quick detour north on 99 to Left Coast Estate. Because you're mid-week, you may have to make an appointment to taste, check their websites. When in Silverton, for sure go to Silver Falls State Park - beautiful hikes, waterfalls, etc. It had a wildfire last year, I haven't been up to see if there is visible damage, but it's usually the Oregon mossy green people think of.
Drive from Silverton to Columbia
If you're wanting a backroads drive, you can certainly do that, but my quick Google map shows a 3 hour drive that way, plus there were massive wildfires through that area last year (Estacada) and I'm not sure how scenic it might be. For efficiency, I'd instead cut up through Oregon City (my hometown) and over to Sandy and up around Mt. Hood. The drive between Gov. Camp and Hood River is called the "Fruit Loop" with lots of produce stands (though you'll be a little early for apples). I also suggest staying in Hood River and make the day trip up to Maryhill. On the way there, drive on the historic Mosier-Rowena Highway 30 to the Rowena Crest Viewpoint for one of the best gorge views. Before you go to Maryhill, be sure to do the quick side trip to the Stonehenge - it's quite unusual and has good views. I've not been there but there is a winery in Maryhill that serves food. You could drive back on the Washington side and cross back into Hood River.
Hood River to PDX
The historic Columbia River highway is a delight (and very narrow!) but is in a constant state of unexpected construction or closure. Check tripcheck.com for the latest info. Tons of hiking opportunities, but this area was burned in a wildfire several years ago (sense a theme?) and some trails may not be fully accessible. If you stop at Multnomah Falls (or any trailhead) make sure nothing valuable is left in the car - break-ins are sadly very common.
As always, PM me if you have questions. I kind of like it here :)