by train from Krakow to Wroclaw to Zgorzelec/Gorlitz, any advice

I have been to all of these places by train though I visited Görlitz on a separate trip (from Dresden). I walked across the pedestrian bridge to Zglorzelec just to have a Polish meal. But the Zglorzelec is much less prosperous than the German side, at least the part right on the border. I had only a night and didn't get too far into Zglorzelec, which I suspect has more charm further away from the border. But Görlitz on the German side is a lovely town.

You might be disappointed looking for scenes from "The Grand Budapest Hotel" in Görlitz however. You can find them - I found a few, but although it was kind of cool, it was mostly just a shrug. Don't go because of that.

I think the trains between Krakow and Wroclaw have been improved since I was there in 2012. You should be able to get direct trains place to place, easily. I don't care for long-distance buses (which can be cheap and just as fast, sometimes faster than the trains), but if they work for you and you don't love trains as much as I do, buses might be OK too.

Be sure to see the Racławice Panorama in Wroclaw - a circular painting depicting a famous (and rare) Polish military victory over Russia in the 18th century. I guess this isn't the first or only circular painting in history (maybe it used to be a "thing?", but I found it really unique and interesting. There is a museum in Wroclaw mostly devoted just to this painting.

You can certainly get to Goerlitz by train from Germany; I traveled there from Dresden. From Poland there is service from Wroclaw, sometimes with a change in Wegliniec.

I don't know whether Goerlitz will work well as a base for trips witjin Silesia. You can start by seeing whether Rome2Rio.com thinks there is rail or bus service to the places you want to go. Do not trust Rome2Rio's information about frequency, travel time or fares, but it's usually correct about the existence of service. You'll need to click through until you find the names of the transportation companies providing the service so you can go to their websites for more reliable information.

I'm sort of doubtful that there are bus tours of the sort you're interested in offered from Gorlitz, which isn't terribly large and doesn't seem to get a lot of tourists. The fact that you're talking about destinations in Poland (I think) makes public bus tours out of Goerlitz less likely. I'd sugest doing some Googling; that might turn up something. If you have no luck there, see if you can find something out of Wroclaw or Katowice. The good news is that something originating in Poland will probably be less expensive than something operating out of Germany.

I just travelled Silesia as a slow trip to Lviv, starting from Dresden, and could do everything I wanted to do by train. Use the train planner of the Polish railways. The present schedules give you a good indication. Check the schedule at a date close to your actual travelling for changes.
An interesting WWII site is the radio station of Gleiwitz/Gliwice, where the Germans fabricated the incident to justify the attack on Poland in 1939. It is a straightforward 20-minute walk from the Gliwice train station.
Possibly the best memory are the two so-called Churches of Peace in Jawor and Swidnica, with the one in Jawor the least visited, but the most impressive. Both remarkably easy to reach by train from Legnica, but probably also from Wroclaw, although that might take a little longer.

My wife and I did this just a few weeks ago! We found the train schedules between Krakow and Wroclaw were limited during the time of our visit (early May 2018), and the times were longer than I observed on my preliminary research (during which I did not insert the exact dates). I did a quick search just now and it looks as if that is still the case. I think it was due to track work near Krakow Glowny. So train was not a good option for us on that leg. The bus was around 2.5-3 hours from Krakow to Wroclaw. Be aware that the legroom on buses is not that great (worse than a coach airline seat), and show up early to claim a good seat--i.e. so you and your travel partner can sit together, and the one of you with longer legs can sit in the aisle seat. We stopped off for several hours in Wroclaw, storing our bags at the station (train and bus stations are right next to each other in Wroclaw). The Wroclaw old town is quite a walk from the train station, but if you have the patience to figure it out you can easily take the tram (we did on the way back). Goerlitz is awesome, a great vacation from your vacation. Not much happening there but a very pleasant walking town. We stayed at Hotel am Goldenen Strauss, directly across from the former department store that was the hotel interior in the Grand Budapest Hotel. I think we were 5 hours in transit in total, can't remember exactly. But breaking it up with a day visit to Wroclaw, it was very manageable.

Thanks to all who have replied. All your responses were helpful and from them I was able to develop a realistic itinerary. I’m still thinking about Gorlitz.
I’ve researched mileage and time for the wooden churches that I would like to see. The starting point will be Wroclaw. I’m hoping to hire a knowledgeable tour guide with car. See June 24 email re details of my day trip itinerary.