It's all down to personal preference, my comments regarding the auto were tongue in cheek and they are perfectly nice to drive in a wafting and relaxing sort of way. There is no difference in terms of fragility between auto or manual so that's not something you need to consider, both are very strong and reliable transmissions and you certainly don't need to thrash the 2.8 in either version to enjoy it. The Italian market 2 litre version is rather different as it was only available with a 6 speed manual (even when the 2.8 still had a five speed) and it thrives on revs but that makes it much more of an occasion and its actually faster than the 2.8. The 2 litre car is actually a well kept secret, they're 95% as good as a Cup but 1/3 of the price
Its quite an involved process as there are a number of significant differences between the various versions. Obviously you'd need a gearbox, pedal box, clutch master and slave cylinder etc but you also need to consider that the auto differential is different to the manual as is the propshaft so both would need to be changed for the manual versions. The flywheel would need to be carefully sourced as there are several different versions depending on the number of bolt holes on the crankshaft and there were also several different clutches which are only compatible with certain flywheels. The ECUs are also different between auto and manual so they would also have to be changed, as would the centre console (gear lever surround) and you would have to disable the inhibitor which only allows the car to start when in Park. Its all doable but finding the parts would be difficult and with all the issues surrounding the various mechanical components it would probably be easier to swap out the entire engine/gearbox assembly from the donor car rather than just swap the gearbox. With all that in mind it would probably be best just to buy a manual car in the first place.