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I'm having trouble finding and sticking to one word to indicate whatever value the user intends to use with my instructions.

For example:

Select your preferred printer.

I'm wondering what synonyms for "preferred" you would use in such a situation.

Would something more direct like "target" be more fitting? Such as:

Select the target disk.

In short, how do convey to the user that this is the time to enter preferences and not some data that they may have missed earlier?

One possibility is to not use the adjective: "Select a printer".

Another is to use the adjective appropriate to the action: Sometimes you mean "Select a disk", sometimes (like for formatting) you mean "Select the target disk", sometimes (for installing an OS) "Select the desired boot disk", etc.

I wouldn't look for just one word. "Preferred" is sometimes valid, if we are talking about generating a report, "From the options presented, click on your preferred settings".

In that case it sounds better than "click on your target settings" or "click on the settings".

But when you are erasing files or a disk, "preferred" sounds wrong, you are taking an action on something and "target" is more appropriate: "Select the target files". Or even make it more explicit, "Select the files to be erased".

Don't feel bound by pointless consistency, your objective is to be clear to the user, you get no points for consistency of word use.

All instructions writers wrestle with these terms. Just remember that instructions should be absolutely clear, without ambiguity. "Preferred" can be ambiguous. Does a "preferred" printer stay that way? Are you referring to a "preferred" printer, or just a printer to use now?

Select the printer to use (for whatever you are doing).

Avoid "desired" and similar words that imply emotional choices.

"Select the printer to use" is about as clear and concise as you can be. Most importantly, you may have to explain what a "preferred" printer means, because that's the word in the software interface or existing documentation:

"Select a printer from the Preferred Printer list. Documents will be sent to this printer unless it is not available. In that case, documents will be sent to the Secondary Printer."

When graphical user interfaces were new, there were prescribed terms: You select an object, text, or item to be the target of an action. Selection is a "ready" state. Then, you choose a menu command or click a button to apply the command to the selection.

GUIs have evolved, and newer writers don't always observe these distinctions. If you haven't done it, check out the Apple and Microsoft style guides for technical communication.
And this, for all the right names of things in the Windows UI:
https://docs.microsoft.com/en-us/windows/desktop/uxguide/text-ui