For fishing Baker Bay you should put in at Ilwaco or Chinook. Tricky getting out of Chinook. You can put in at Deep river and follow the channel markers out and fish down to Portugese Pt. or the flats anywhere in between (it can be tricky if you don't know where you are going with the channels shifting and the sand bars). The unimproved launch mentioned earlier is do-able with a boat like yours but you better have 4x4 and put in and take out around high water. For upstream, just put in at Cathlamet, where you can easily fish miles of river down towards Deep River.
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Chasing old rags 500 miles from home.