@nest0r
It's not that bad. Actually, if you just set your computer into JP mode, and type out the romaji in kana mode, remembering to hit space to convert the proper kana into kanji, it's not so bad. Just remember-- no spaces in Japanese text, and some of the things she uses, like "-" in "sanji-han" aren't to be typed in. It's not ideal, but it can be done. Do that in the 'add cards' section of anki, and it'll auto-generate the plain hiragana reading. (You'll have to remove the odd homonyms, though, which Anki will put in {}.) Then just copy and paste both into whatever spreadsheet you want to.
The thing is, romaji is just spelled-out kana, with a few variations you'll figure out as you go along. There's a good thread in here somewhere about Japanese text input with more details. Romaji is the Devil's Work for studying, but it has its uses in a pinch.
She doesn't use a lot of obscure kanji, so it's not to hard once you get the hang of it.
Of course, I use a pen scanner, so I'm skipping all of that anyway. >_>a
I have to say, using a scanner/OCR of any kind makes the process an order of
magnitude easier/faster, with fewer errors introduced into the system. Best $300 I spent, even if the manufacturer is flaky, and I probably overpaid by $100. If you are going to scan a lot of books, OCR is probably the way to go.
Oh, and How to tell the difference between Japanese Particles does NOT use plain kana only. It also uses -sentence in full JP/romaji/English translation. But it's still an excellent book.
@ghinz--
JFE has already been converted into an excel spreadsheet. Just check the JFE thread.
There are a lot of good books on particles in general. I've picked up a few over the years, and none of them are terrible. It's more of a matter of how they're organized. AAP is just done particle by particle, which isn't the most effective way to do it, but it IS thorough. I looked at the dictionary of Japanese particles, and it didn't offer any greater advantage that would be worth not using my scanner-- the boxes it uses screw up the scanning. It's a good book, but it's not that good.
HTTTDBJP (lol, great abbreviation there, huh?) groups them by function. Japanese Particle Workbook (which is pretty good, too) groups them by frequency, also a valid way to approach it.
It's kind of a toss-up between the latter two, in my opinion. AAP is nice just as a source of extra sentences, but it really does lack a functional approach that would make learning more meaningful, as does the dictionary. They're both better reference books than a study guides, if you ask me. (Then why the hell have I been scanning AAP? LOL.) Actually, I checked AAP out of the local library and started mining it, but I stopped after a couple of hours when I realized that trying to mine all of the sentences out of it and group them into a more logical fashion was too much work. I went and bought a copy of my own as a reference book, though, because it's good for that.
I still can't decide between the other two books. They're both good. Right now, I'm going to finish UBJG first, then decide later. But if you guys pick one of those two, let me know, and I'll help out.
For the record, I've just been scanning UBJG straight into Anki, so I can't really help you there. UBJG is a good book, if a bit dull and repetitive. I don't tag my cards, so at this point, figuring out which sentences in my deck are from UBJG would be like trying to unscramble an egg.
EDIT:Sorry to post right after myself, but if you wanted skip the novel above, here are my thoughts on the books suggested:
--AAP/Dictionary (discussed that above.) Not in favor of that.
--KIC I'm not at the point where I'm even close to ready for that. Tough for people who want J->E translations, and KIC skips a lot of compound in its sentences.
--Genki -- I tried mining it, and quit after 6 chapters. (It was my old JP text in college.) I'm sure there's material there, but it's probably more trouble than it's worth. Also suffers from "Textbook Syndrome"-- language you'll never use, similar to UBJG, but UBJG is straightforward and easy to mine.
--JFE -- already in a spreadsheet-- see the JFE thread.
--MNH -- never used it, but it's a textbook. Not really a fan of those.

--Dict of Basic/Intermediate J Grammar-- I'd have no idea how to approach the material. Alphabetically? That sounds a little nuts, if you ask me. Great reference books, though, and useful as something to check for answers... *maybe* I could see using a textbook, if you used it as a framework to order the Dict of BJG/IJG with, but without a framework, it's just pile of information.
I'd say if you want my vote, it would be for How to tell the Difference between Japanese Particles, just from a functional point of view. Mine both the example sentences, and the quiz sentences, with the answers filled in. JPW is also a good book, but it may be harder to find that HTTTD.
I'd also recommend UBJG, but I can't help you much there.
The Kodansha Sentence Patterns books would be useful, too. Either one.
(Yes, I have a crapton of books. Kodansha must loooove me.)