Rhine suggestions in September? (and more!)

We had such a good time in the Mosel Valley and totally by accident. Wanted to be close to a weekend "Strassenweinfest" so booked in a "Weingut", a mom & pop winery with just a couple of guest rooms. September is harvest time, so there will be lots of these festivals up and down the Mosel Valley. This was the lowest cost and best quality of 3 weeks in Germany. They have rental bikes and a nice bike trail along the river in a disused railroad bed.

Strassenweinfest is a village street wine festival, with all the local winemakers with booths selling samples of their wares. Add in two or three "marching" bands and it is a wonderful party. The best bands are from Holland and play for glasses of wine at the various booths.

Use the dynamic event calendar to find events when you will be in the neighborhood.
http://www.mosellandtouristik.de/en/culture-events/wine-festivals/

Where do you depart Germany? Guessing Frankfurt? For me personally, I would cut days in Prague and add them to Berlin. There is so much to see and do there, that 4-5 days is better.

Check town websites to find events like wine festivals. They will be highly publicized. Most popular towns are Bacharach, Ober-Wesel, Sankt Goar, Eltville, Rüdesheim, or Boppard. You may find other smaller towns in the Rheingau holding festivals too. Places like Kiedrich, Lorch or the near-by Limburg.

Use the train and buses if you are visiting fests and drinking. Driving after even a glass or two is dangerous.

"We like to eat good food, drink beer or wine, take photographs, and hike/cycle(something active)... I'd love to know which towns and activities you'd suggest for the 3 days in the Rhine area..."

I'd pick Boppard for a base town and venture out from there. Boppard has a nice selectioin of eateries everywhere you turn:
Riverfront: http://www.jazclass.aust.com/blog/photos29/blog273.jpg
Weinhaus Roemerburg - https://upload.wikimedia.org/wikipedia/commons/9/97/Boppard_Weinhaus_R%C3%B6merburg.JPG
Severus Stuben: http://media-cdn.tripadvisor.com/media/photo-s/02/e0/0b/ce/severus-stuben.jpg

Take the chairlift (or hike) to the Vierseenblick lookout where the river looks like 3 lakes; a series of trails gets you around the top of the hill - Gedeonseck terrace is just a few minutes walk from the lift:
https://s3-media1.fl.yelpcdn.com/bphoto/T9oxNMwLvt_-r5nCsce-jg/o.jpg

Try the Klettersteig? http://www.damscheid.de/typo3temp/pics/3d5d833b9b.jpg

Boppard is well-positioned for outings. St. Goar's Rheinfels Castle is just to the south. Park in town and walk up for some exercise and views, or hike the trail south or north from the castle that skirts the cliffs for more great views. You'll find some rest stops at lookouts, like this one:
http://www.camping-loreleyblick.de/neu/bilder/AussichtsplatzPilz_IsabelSteinhaeuser.jpg

St. Goar's sister town to the south is Oberwesel - walk the old town wall there:
http://www.oberwesel.de/en/wandern0/stadtmauerrundweg/

You can also walk up through the vineyards to the Guenderodehaus, the film set for a popular German TV series called Heimat, for a glass of wine and some outstanding views:
http://www.christiane-geldmacher.de/wp-content/uploads/2014/09/rhein2014-003.jpg

(Actually you can hike the cliffside trail between St. Goar and Oberwesel in about 2.5 hours and hit the G'haus en route. Great hike.)

From Boppard ferry across to the Filsen dock and drive north to Braubach for Marksburg Castle, the only never-destroyed medieval castle you can tour on the Rhine. It's great - and you'll get some cardio if you walk up here as well:
http://de.travello.com/f/p/2011/06/29/40744.l.jpg
http://www.marksburg.de/en/
Enjoy Braubach's old town too:
http://djtravel.homestead.com/files/braubach_-_hotel_1610.jpg

From Boppard you can take an outing to some of the Mosel towns as well. Cochem and Winningen are lovely.

http://www.der-takt.de/typo3temp/_processed_/csm_NEU_T_Reichsburg_Cochem_3_087e83a8d1.jpg
https://s-media-cache-ak0.pinimg.com/736x/1c/ea/65/1cea658d28a5ad14dd2874c406bdc209.jpg

Thank you everyone!! You all gave such great suggestions! I truly appreciate the time you took to reply.

I like the idea of staying in Boppard and traveling out from around there. I Think we'll do that for a couple nights. We found out a friend is moving to Mainz so we will also spend 1 night there. This sounds perfect to me!

Afterwards we're heading towards Berchtesgaden!

Thanks!