Trying to tie 4/1 days in Prague with outside trips..

You got only 3 full days in Prague. Non of your day trips is really doable in half day if you want to see something. One suggestion; stop in Cesky Krumlov on your way to Munich. Yellow bus Prague to CK - about 3 hours. CK to Linz by shuttle then train to Munich. To get to Konopiste about 2 hours; one hour to Benesov then walk or take a little tourist train (it goes on the road). To Olomouc about 2 hours by fast train Pendolino then by tram to the downtown. To Kutna Hora about 1 hour by direct train to the Main Station. Ossuary in Sedlec (part of Kutna Hora) is about 1 km. Walk or take a city bus. Then from ossuary it's a long walk to the center of the town or you can take a city bus. All of it takes longer than you think and all of your day trips will be full or almost full day trips. Don't you want to have some time to see Prague? In that case you would have to drop at least one of your destinations.

It might be worth considering doing an organised trip to kutna Hora as Ilja says it is a trip that needs most of a day especially if you are organisng it yourself.I have been to Kutna hora several times , last time was in Novmber last year and on all these trips i needed most of the day.
Also with Konopiste easy enough to do on your own but time consuming to get to and from the place. I have visted there on my own easy enough but one time a few years ago myself and 2 friends took an organised tour to Konopiste and also the Kozel brewery, I think we left about 9.30am and were back in the city about 2.30pm

Y'all are correct. Cant do it all.
We arrive first day at noon from Regensburg/Nuremberg. I figured free tour, stop at a few sites before the "ghost tour".
Next day ("1") take the very early train to kutna hora for 8:00. Spend 4 hours and be back before 2:00 and do sites in Prague.
Day "2" spend entire day in Prague.
Day "3" Konopiste and Prague.
We depart for Vienna around 3:00. So that fives us another half day in Prague for about 3 total.
I realize we cannot possibly see everything in Prague or surrounding areas, but that is another reason to return. :)
Were also not the sort to walk for hours shopping. We like to hit and run...

sounds reasonable to me as long as you get out early.
I first visited Prague over 20 years ago and have been visiting ever since.I am lucky enough to only be about 2 hours away by plane and with low cost carriers flying from my home airport and being in a job that allows me a lot of paid hoildays i get to visit Prague at least twice a year.
I hope you have a great time in the city and the other places you visit and that the sun shines for you.

I put this up on another thread on Kutna Hora but it is my Trip Advisor contributions to the Kutna Hora section, a few reviews and a lot of pictures you may enjoy. I was last there in November with some friends from the USA one of which lived in prague for several years.
meeting up with a couple of the same friends next month to enjoy a few beers in our favourite city.
http://www.tripadvisor.co.uk/members-citypage/unclegus/g274701

Llja, I meant we leave the US for Munich this Thursday for the first leg of the trip. Were so excited!

I appreciate the advice. We are always flexible and just figure something else out.

Train may not be the fastest route to CK, but it allows you to stop in Benesov en-route. Luggage storage in the station? - I don't recall, but you can always ask some friendly-looking person. If you are going to walk from the train station to Konopiste castle, be sure that you understand the system of path markers on the trees; a taxi would be easier. The weapons collection is amazing.

the walk to Konopiste castle from the train station is quite easy, takes abour 25-30 minutes, go out the station keep left and walk over the railway bridge and follow the road. it is not an unpleasant walk.
you can see the route here.though it looks like you are walking on road all the way most of the path is slightly away from the road along pleasant fields.
https://www.google.co.uk/maps/dir/Bene%C5%A1ov+u+Prahy,+N%C3%A1dra%C5%BEn%C3%AD,+Bene%C5%A1ov,+Czech+Republic/The+Konopiste+Castle,+Bene%C5%A1ov,+Czech+Republic/@49.7818559,14.6725045,15z/data=!4m14!4m13!1m5!1m1!1s0x470c7fa3db140389:0xf295f49973bcd50!2m2!1d14.683055!2d49.779845!1m5!1m1!1s0x470c7f85e146392f:0x9c7259dcfe00969c!2m2!1d14.656592!2d49.779532!3e2

Are they're taxis to the castle or it is only by path? I can only walk for short periods of time.

Are they're taxis up to the castle or it is only by path? I can only walk for short periods of time.

Yes, there are taxis which bring you to the castle from the station in Benesov.

Great news. I really wish I could hike like I used to.

There is also the tourist train.
http://www.ekovlacekbenesov.cz/en/
looking at the train I think I would rather walk.