About Delete not working in terminal: Use the key "KP_Delete" for the delete key mapping instead of whatever the more intuitive one was called (I already forgot the name of the other Delete key for xkb). That's the one I've been using for years on my N900 and it works perfectly, near as I can tell, everywhere.

...this is the first time I've seen someone post a way to get around shift+fn+[j/k or z/x] printing both letters... You are awesome. Now I might need to rethink my layout, given this new information.

For the record, another way (just reiterating even though it's in the wiki, for those who don't read that part of it), if you find hitting both shift and fn simultaneously a lot more natural, is to simply leave one of those keys at the fourth level completely unmapped. Then it works to just print the one key, for either of the paired keys.

These key mappings are at the X level - they apply to everything that uses the X windowing system or whatever the proper term is - in other words, keyboard remappings and other modifications in the xkb directory apply everywhere on the N900. Every program that takes keyboard input. The only place this doesn't work for that I've seen is the framebuffer console. I don't know of any way to get to console other than at boot on the N900 at the moment though - so this only applies to things like boot-time recovery shells for the time being.

That said, I believe programs COULD override this behavior. Now, to answer your query, with a keymapping that doesn't alter ctrl+[arrow] specifically, MicroB still uses those as tab and shift-tab. Modifying the xkb behavior to allow ctrl+key combos would require you to also modify the file where the groups are defined. Then you can test if Micro-B still overrides... The N900 I'm on with at the moment is about to lose battery power, so I'm going to edit this post from another one as soon as I've re-found where the keygroup behaviors are defined.