Well, the best I can offer is to describe the sequence I used the last time I built a three-masted, full-rigged ship model. That was my little scratchbuilt frigate Hancock, quite a long time ago.
My biggest enemy when it comes to ship modeling is monotony, and monotony comes from repetition. So I tried to space out various activities to produce as much variety as I could.
I started by building the bowsprit - off the model. I like to clamp the spar I'm working on in a vise and finish as much of it as possible on the bench, away from the model (for several good reasons). I built the cap, the bees, and all the fittings that I figured would have been on the real mast before it was stepped. Then I stepped it, and set up the standing rigging (including gammoning, bowsprit shrouds, and bobstays).
Then I tackled the main mast. My theory was that, being bigger, it would be the easiest in terms of technique (I was inventing techniques as I went along), and that it would make the fore and mizzen masts seem easier by comparison. I made the main top (quite an exercise; it ended up having fifty or sixty pieces in it), and mounted it on the mast - along with all the other gadgets that I figured would be in place on the real thing before it was stepped. Then the main lower standing rigging (stay, preventer stay, shrouds, and those infernal nichrome wire ratlines - much easier to rig when there isn't much other rigging to get them tangled in).
Next the fore lower mast and its standing rigging (which took about half as long as the main mast). Then the mizzen mast (which now seemed ludicrously simple) and its standing rigging.
What I did next probably differs from the sequence most modelers use. I made the main yard, complete with all its details (including studding sail booms and irons). I clamped a piece of dowel the same size as the main mast in the vise, and rigged the main yard to it with the truss. Then, using the descriptions in my references, I secured all the necessary blocks and other fittings to the yard, mounted the footropes (from brass wire, so I could make them droop) and made the main course. I rigged as much of the running rigging as I could, and furled up the sail, before transfering the yard from the dowel to the model. Then I added the braces, jeers, and other running rigging. Such lines as the clew garnets, buntlines, sheets, and tacks were already there; they just had to be belayed.
Then the fore lower yard and its sail and rigging, then the mizzen, with the crossjack and lateen yards. (Until the mid-nineteenth century the crossjack yard didn't have a sail on it.)
One advantage of this plan is that it forces you to rig the various lines much as the real ones were. If you get into a situation where you can't set up a piece of rigging on the lower mast before the topmast is in place, you've done something wrong.
Then the topmasts (in the same order - main, fore, mizzen), their standing rigging, and their yards and sails, the topgallant masts and their yards and sails, etc.
This sequence let me switch back and forth: making a spar one evening, making the sail the next, rigging it the next, then making another spar, etc. I was particularly grateful not to have to prepare all the rigging blocks and deadeyes and once. I used britannia ones from Bluejacket; the sequence for blocks was: clean up and drill out (including a few extras), thread on a piece of wire, spray with Floquil primer (no longer among us, alas), brush paint (brown), let dry, remove the wire, rig. Doing that a couple of dozen times is bad enough; doing all of them at once would have done me in. I think the total number of blocks and deadeyes in the model approached a thousand, but I never had to confront more than a couple of dozen at a time.
One interesting rigging feature that some modelers ignore: the staysails. I rigged each of them as soon in the sequence as I could - the topmast staysails as soon as the standing rigging of the topmasts was done, etc. I found that an interesting part of the job, and not especially difficult.
Last came such things as flag halyards, boat tackles, and other miscellaneous gear - and that freakish little flagstaff at the stern with the tiny lateen sail on it. (That one was a real brain buster, and I still have no idea whether I got it right or not.)
Tht's not the only way to do it, of course, but it worked for me (i.e., I actually finished the model without getting chased down by the boys with the butterfly nets). For the benefit of those who haven't looked at my three-year-old thread about that model, here are a couple of pictures of the results: http://i1360.photobucket.com/albums/r650/jtilley1/38900015_edited-2_zpsc2ed8d33.jpg
http://i1360.photobucket.com/albums/r650/jtilley1/38890030_zps5e61656c.jpg
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On my current project, a fishing schooner of about 1912, I'm thinking seriously about making all the spars (there are only about ten of them) and their fittings all in advance, and then setting them up and rigging them. For this particular type of model, that seems like it might go faster and be more fun. Also, the fittings are going to involve quite a bit of soldering. I only want to set up for soldering once, if possible.
Hope that helps a little.