I've seen the system wide tools (that all seem to just manipulate the default key bindings) that allow you to swap keys around, but has anyone found a way to swap keys for just one application? (no, the app in question doesn't offer it, and the author was a bit of a prick about it when I asked if they could enable an option to adjust them.)
I'm talking about real keys like home, end, page up, page down... not shortcuts.
Keyboard Maestro might be your thing. Make a new command group which only applies to the application in question, then for each key you want to remap, make a new command with a hotkey trigger set to the real key and an "Insert Text" action set to what you want the key to be.
The only shortcoming I've found so far is that it can't handle the in-built volume control keys on an Apple keyboard. It can detect them & act upon the event, but it can't suppress the volume change. In fairness, nothing else can either. Most programs I tried can't even detect it. Keyboard Maestro is the king of the pile.
I've been using BetterTouchTool for years and am constantly amazed at its flexibility. Despite its name, it is capable of intercepting/altering keyboard events as well, plus allows you to limit key mappings to particular applications.
You can use Ukelele to make your own keyboard layout, and switch to it when you open the application.
If it's a menu item, you can create a custom shortcut in System Preferences>Keyboard Shortcuts>Application Shortcuts. It lets you (re)assign any menu commands to whatever keyboard shortcut you want, for a specific app only.
Application Shortcuts exist