Hi Roy,
My husband and I did a very, very similar trip as yours for our honeymoon. Parts of France including Burgundy (we stayed in Beaune) and Alsace, followed by Murren and Lucerne.
A few pieces of my advice:
We stayed in Murren for 3 nights and that was plenty. One more day and we would have been a little bored, perhaps because of the weather. We aren't huge hikers, though we did do one day of serious hiking for us. Spent another day hiking down the mountain to the small town of Gimmelwald (which is Rick Steve's favorite Swiss town...he has featured it several times on his show) and then into the valley of Lauterbrunnen. That hike was just delightful. If you go to Gimmelwald (which I recommend!), be sure to visit the "cheese lady". She has a cheese hut across the street from her house; her front door has a sign that that says "Ring bell for cheese". You'll be glad you did! We spent another half-day going to the top of the Jungfrau which is a must if the weather cooperates. Like I said, the 3 days was plenty for us in Murren, but if you are a serious hiker, then 4 might be good for you. Before going to Murren, my husband and I got rid of our rental car in France before heading to Switzerland. There was no need for it in Murren and Lucern. Murren is just a small town, easily walkable and there are very few cars (in fact, I'm not sure they are even allowed there). The only vehicles I saw were delivery vehicles. We took a train, followed by a cable car to get to Murren. We stayed at the Hotel Alpina in Murren - another one of Rick's recommendations. The room itself was quite basic, nothing fancy. But the view---oh goodness. Jaw-droppingly beautiful. The hotel overlooks the mountains and the valley below....in my opinion it has a better view than some of the 4 star hotels in the area, as some of those hotels are across the street and just don't have the same access to the view. The hotel owner, Roger, was very friendly and accommodating.
We stayed for two nights in Colmar at Chez Leslie (a B&B that Rick recommended in his book). It was a very nice B&B....good breakfast, well kept accommodations, close to the downtown area. Our room even had a balcony....request that ahead of time, if you're interested. We used Colmar as a base for going to Eguisheim, Riquewihr, and Kaysersberg, as well as Strasbourg. Eguisheim, Riquewihr, and Kaysersberg were amazing....truly must-see towns. They were my favorite part of Alsace; each town had its own flavor and flair, and each was more adorable than the previous one.
In Beaune we stayed in a bed and breakfast that Rick recommended, though I can't recall the name. Beaune is a wonderful spot for taking day trips from. I remember driving out to the town of Pommard and visiting a vineyard there, and we drove along a route that Rick recommended in his book which was scenic and beautiful and had several wineries along the way to stop at. On our day of driving around outside of Beaune, we got ourselves some food in Beaune for a picnic lunch and then stopped for lunch at one of the many beautiful sights you will encounter. We also visited Chateau Rochepot in Burgundy; that was a beautiful castle (another Rick suggestion). I had only two days in Beaune, and I wish we had had one or two more days. So it sounds like you will have a good amount of time to see and do a lot.
Your trip is going to be truly fabulous!