If you've got your heart set on a Manual, then buy one with a Manual, job done, converting a Auto to Manual can cause issues, apart from the work involved, you wont have to worry about having to change Diff ratios, ECU Mapping, Loom, Autobox Speed Sensors etc to get the car back to standard.
Ive driven and owned quiet a few Omegas now, mostly 3.0/3.2 both Auto and Manual, nothing wrong with Manuals if your not fussed about using the 3rd Pedal which would always be my preferred choice.
3.0 Manual are a good drive I would happily get another, 3.2 Manuals pretty much the same but with slightly different Engine characteristics, R28 Boxes on the 3.0 Manuals, slightly Stronger R30 on the 3.2 both have 3.7 ratio Diff, both do what it says on the tin. Only slight downside is the Gear Stick throw is a bit wide on the Manuals, if its an issue for you, can easterly be sorted by fitted a Short Shift Stick and bending/angle it towards the Drivers side.
I'll be keeping both my 3.2 Manual Specials for a while yet.