Oh... I totally get it. Packing the Klingon font in the book is the way it ought to be. I'm just sayin'...
I'm not sure what the spoiler picture is demonstrating...
BTW, I have a touch 5.3.2. Your klingon.mobi does have Klingon glyphs in it. But it doesn't always work right; lots of Klingon show up, but the rest is stacked Tibetan characters (which, at 2am, seems half funny, half profound).
And that might be the problem. Klingon lives in the private use area of Unicode, and so does everyone else's great idea for a glyph. Tibetan has it's own range, so the fact that Tibetan stacking characters show up instead of Klingon suggests to me, anyway, that the Tibetan font put pre-composed stacked characters in the private use range, for, well, private use. I've also seen little-used Chinese characters showing up in the private use area until I set the font to what I put in /mnt/us/fonts, and they're from one of the stock CJK fonts. So maybe your Klingon is just getting stepped on (poor Klingon).
Hard to be sure without more tinkering. Do you have fonts in /mnt/us/fonts? It might also need 5.3.2. ?.
Annoying, but possible approaches, would be remapping your Klingon font to a range not used in stock kindles (maybe to Tibetan? Klingons would like that.), replacing the Klingon with html entities just to see if they survive through mobi/kindle gen better.
Good Luck! Kaplagh, or whatever!