Mid-day, the ferry wait shouldn't be that long, especially on a Monday. The ferry departs every thirty minutes. Once on Whidbey, if you don't stop, you can be in Anacortes in about 45 minutes. So depending on when and where you stop, your leisurely arrival in Anacortes could be late afternoon to early evening. Since you're doing this in late June, you're at the time of year when we have the longest days. It won't be dark till around 9PM, so you'll have lots of time to explore your way up Whidbey. Staying two nights in Anacortes makes a lot of sense, so you'll have time to work your way through the shops and such in Anacortes that next day. No sense rushing things, so departing Anacortes the third morning makes the most sense. Figure it's about three hours driving time from Anacortes to Winthrop, plus stops along the way. So you'll arrive in Winthrop/Twisp area by dinner time. Perfect time to arrive there, without feeling like you rushed to get there. I think your plans are good.
Dave