TL;DR: Reach out to them and explain that you need to work things out with them beforehand.
Note: I'm assuming a Modern Orthodox level of Judaism. This is based on my own experience, as a Modern Orthodox Jew.
How do I communicate to my jewish friends that we are already aware of some rules regarding their religious obligations, have made some arrangements and some accommodations, but need their feedback and other specific needs?
(emphasis added)
I'd like to start with saying one thing: Don't just do something based on your knowledge of the religion without consulting them first.
You mention that you'll be getting rid of "obvious non-kosher foods". Okay; that's great. But do you need to do that? You can eat the food. It's not a problem for it to be in the same house as them; they simply can't benefit from it themselves. It's not like they can even eat from your dishes in any case; you'll need to either get new dishes, have your friends tovel them (immerse them ritually in natural running water), and keep them separate from your regular dishes... or just buy disposable plates for the time that they're there.
(They also can't eat any of your food; unless it's explicitly got a hechsher (sign of Kashrut), they can't eat it anyway, fruits and vegetables aside (which have their own issues that I can't get into).)
You need to reach out to them about this. Figure out together what you're doing about utensils, plates, etc, as well as figuring out how they're going to find food to eat. Do not assume that your own preparations are sufficient.
The other thing you mentioned was Shabbat. This is a really tricky situation, because of the sheer number of things to take into account. Your town may or may not have an eruv - a string that runs around the entire town that allows Jews to carry items through the street - so they may or may not be able to carry anything in their pockets on Shabbat. Bear in mind that they also can't walk more than ~1.2km away from the city in each direction on Shabbat and that they can't use transportation.
Again, reach out to both your guests and the local Jewish residents. Inquire about the eruv... but make sure that you don't make any plans around this without consulting your guests first.
There are other things to consider as well - such as the fact that they're not allowed to explicitly ask you to do something that they can't do themselves on Shabat unless it's for the good of an entire community. After a meat meal, they have to wait 6 hours before eating dairy. There are prayers in the morning, afternoon, and night. There are many more such examples.
These are just a few things.
The point of this was to illustrate that you can't rely on your own assumptions and research. Don't assume that whatever precautions you took are good enough without discussing it with them.
I assure you, if you just call them, state honestly that you need to talk to them about the trip, and have a discussion about what they need - they'll both appreciate it, you'll learn a lot, and you can both plan ahead for the trip to make sure that it's enjoyable. Be honest and open to ideas, and most importantly, respect what they say if they say that something won't be possible or that they need to do something at a certain time. Trust their judgement over yours.
Also, as @DavidK points out in the comments, some people don't adhere as strictly to certain laws. It's entirely possible that you'll be planning for something completely unnecessary if you try to make preparations without consulting them. You have to work with them to figure out what you need to make accommodations for and what you don't need to adjust for.
Doing this as early as possible is key, so that there's time to make any adjustments or preparations necessary - such as reaching out to the local communities about where to buy kosher food, for instance.
Reach out early, ask them to help you prepare for their visit, and listen to what they say.
