Not too bad a job. Ideally the ECU needs to be told its a 3.2 (or if you use a 3.2 ECU, needs to be told its a manual), but easily achieved via Tech2. The MID/GID/CID/whatever also needs reprogramming (via Tech2) IIRC.
2.6 will have R25 manual, 3.2 manual is R28 and slightly stronger. Depends on the abuse levels you give it I suppose.
R28 was standard on 3.0 Manuals, 3.2 Manual Omegas were fitted with the R30 Box (R30 internals in a R28 Housing), these were a lot stronger and also had a longer Ratios, same Box as the 24V Dti Manual but different Ratios.
If you do the Lump swap and upgrade the Gearbox your also ideally need to swap the Diff as well.
3.2 Manual did have a slightly different Main ECU Map over the 3.2 Auto, as TB says best to Tech 2 the ECU though to tell it its a Manual, they will run without it but you may wake up one morning with a Car that wont start because the ECU cant see an Auto Box fitted.