Yeah, doing it by hand in the text file is gonna be a pain, but certainly a doable fashion if the coordinates aren't a problem for you to work with. Sadly would be for me, but if you can do it, cool beans!
If you've managed to convert the .mesh to something you can import into XSI, then it'll honestly probably be easier to play with them there. (I've done that through 3D Object Convert -> Blender -> XSI, program wise. But doing it that way always lost the UV maps, which means retexturing everything. Not a so much a problem when you're altering stuff enough to need it anyway though..)
From there, if the model still has all it's points, you can just add new ones as you please along with the rest. If not, you'll need to create a new point (the object type is actuall called a null), and name it "rootpoint" (without the quotes of course). The rootpoint goes at location 0,0,0 generally, though I suppose you could just place it at the center of the ship if so desired too. In anycase, all following meshpoints will be using it as their point of origin for their coordinates, so it's easiest if it's at the origin itself.
In the explorer view, the rootpoint and all meshpoints need to remain outside of the ship's model, though all meshpoints go under/inside the rootpoint (kinda like the rootpoint is a folder holding all the other points and such.)
By convention, all meshpoints have a five character prefix of "P###-". This prefix gets removed by the convertxsi.exe file later, so it probably doesn't particularly matter what you put there. It's used for naming meshpoints by the same name, because XSI won't actually allow duplicate names in objects, but you need specific (and thus duplicated) names for Sins to recognize what points do/mean what. (For example. In the .mesh file, you'll see a whole bunch of "Weapon-0" points. Obviously these are all the points for the first weapon in the .entity file for the ship. But in XSI, these points would be listed P001-Weapon-0, P002-Weapon-0, P003-Weapon-0, etc. Oh, and the names ARE case sensitive.)
If you right-click (or double click, I think, I forget) to edit the points, there's an option under Shadow Display > Icon that'll allow you to change what the point looks like. (The Primary Display will change what the point (Null) IS, so you don't wanna change that one). The Arrow options there is really useful for making sure the points are facing the appropriate direction - VERY important with gun points (because their orientation determines which bank they're in) and engines (because it's gotta know which direction to send out those flame jets!) - Just remember that you're essentially limited to 90 degree angles for the banks. Diagonals WILL work (and it helps make the particle effects go the right way), but I'm not at all sure where the cutoff is from one bank to the next. (I'd assume the 45 degree angles, but what happens to those ON that line? No idea, really.) I also don't know how much up and down angles effect it weaponry. - If you don't wanna use the arrow, though, the blue axis (Z) is 'forward', and the green axis (Y) is up. Make sure you always adjust those in Local instead of Global, though. Well, assuming you don't rotate the rootpoint, and that your ship is actually facing the proper direction too (sometimes you just won't know that until after you've loaded it into the game and see it flying backwards/sideways/etc).
As for the point names: (Assume whatever 5 character prefix you add is already in front of these, and replace any # with a number from the range listed in ()'s.)
Weapon-# (0-2) (Direction matters)
Ability-# (0-4) (Direction matters. I've no idea what determines which abilities use which point, however.)
Bomb (Direction matters, same as if it were a weapon)
Hangar (Direction matters for which way the strikecraft launch, and possibly return to)
Above (For those buffs above the ship)
Center (For those buffs from the center.. like the leveling one)
Aura (For those buffs shown under the ship, usually.)
Exhaust (Direction matters)
Flair-Flair_Blink
Flair-Flair_Blink_Small
Flair-Flair_Doubleblink (Direction matters because there's two lights being placed)
Flair-Flair_Doubleblink_Small (Same as above)
Flair-Flair_Bowtiespin (Direction should matter to determine which way it spins, but I haven't personally played with this flair)
Flair-Flair_Lighthouse (Direction matters for which way the "beam" spreads out toward)
And then there's any particle affects that are used, but those names all vary entirely upon the particle file in use, so I can't very well list those since you can make up your own!
Anyway, I hope this helps explain how to do those in XSI a little more, though I'm honestly more or less just paraphrasing the help doc. This is probably easier to understand if someone could actively show you (woulda been easier for me the first time, that's for sure. Hehe), but can't help ya with that part so much.
