1. Constructing manually is a good way to learn the mechanics of the fill, and some choose to remain manual constructors long-term; One can also remain competitive as a manual constructor because good fill can be produced with reasonable effort as long as editors don't drop the word limits below the 78- and 72-word marks. I personally started out as a manual constructor, but switched to machine-based fill as my puzzle concepts required more talent than I could muster with graph paper alone.
2. I own Crossword Compiler 7.1 professional, and there are unranked word lists that come with it that are not so helpful. You can get a wordlist from this website if you are a Gold Member, but the entries are also unranked. It's better to get a mentor who can at least supply you with a partially ranked word list. (The best route to getting a mentor is to join the Cruciverb-L mail list and request one). Other useful software include the Ginsberg Clue List which Matt has provided free of charge. Wild card searches can be conducted there or here: http://www.onelook.com
-- That's all the resources I need to construct these days.
3. If I were simply making a 40-letter theme within a 78-word grid, I'm guessing I could fill it 99+% of the time using software. For a simple grid, mindless fill can be generated automatically in seconds, but I don't recommend that route; Instead, one should select the entries thoughtfully from menus that the software generates for your wordlist. (You also need to make sure that the puzzle isn't too loaded with duplicate entries, excess fill-in-the-blanks & partials and intersecting proper nouns. This requires inspection as the filling process moves along). Although fill can be done in under an hour, it may take 3 to 6 hours to produce fill that is lively and free of flaws. If your word list is poorly ranked, it may take you significanly longer.
4. Since I'm drawn to complicated grids that require a combination of machine fill and manual fill, I can sometimes get 80% through the fill before I find I have to discard it -- sometimes after 6 hours of attention. So be it, I'll try again the next day.
5. See item 2 above. Everything you need is there.