Manual stopping of T mode with the Copal 0 shutter is more than adequate, because the difference between 1min59s and 2min1s is so marginal that it is hardly visible in your pictures given the light condition does not change.
The more challenging thing is the change of light condition which would easily make a big difference even you make two successive shots of accurately 2min each, as well as the moving objects e.g. cloud. The use of PTGui and tools in Photoshop would be required. (Example:
http://voidshatter.tuchong.com/12548173/)
By the way, you have a CCD back, and it is not recommended to use it for dedicated long exposure shots. Reasons:
a) If you use default settings, you have to wait for a darkframe NR after each long exposure, leaving a big gap between your shots, which is more prone to change of light conditions and moving objects; if you disable darkframe NR by setting camera mode to "Aerial" then you get degraded image quality out of a CCD back.
b) ISO 200 vs ISO 35 (though extended) would lose lots of dynamic range, leaving less room to push shadow in post-processing (even worse than Canon), thus limiting the scene you can shoot. Bracketing may not be practical for the necessity of darkframe NR mentioned above (more prone to change of light conditions and moving objects).
Conclusions in short:
I would rather not stitch long exposures. I would use a CMOS back (e.g. IQ350) to do long exposure. The IQ380 is the "best" digital back you can buy at the moment, but it is not appropriate for dedicated long exposure shots. If I have to own the IQ380 and if I can't afford to own both the IQ380 and the IQ350 at the same time, I would just buy a Nikon D810 to do the long exposure job.