Well it would seem that you will usually look at around R15k, but lets say R15-20k to be safe, this may seem like a lot but auto box rebuild will probably set you back the same.
The biggest mission here it the sourcing of the parts and will depend in how lucky you get in terms of finding things. One good thing is the gearbox should not be an issue as I think the gearbox from any other M52 engined car (e36/e46) should fit your car and there should be a lot of those around, if I take a guess I am thinking the gearbox will probably set you back around R2500, this for a 5 speed. 6 speed might be a better idea seeing as you will already be going through the trouble of sourcing stuff, but this will be harder to find and will set you back a bit more, around R4k I would think. Later model e46 330i all came with either 6 speed manual auto or SMG, they do however use the M54 engine but i think the gearbox should still work. Also with a 6 speed you can keep the diff the same, as you will still have lower cruising RPM thanks to the extra gear, but will have better acceleration and response overall.
The you will also need the propshaft, this might the most problematic as you will probably need to find one that came specifically from another manual e39 or you will have to re-engineer your current prop so it is the correct length (or find a spare to do it with), but this is fraught with danger as BMW props are notoriously hard to get right, but it can be done, another possibility is to just buy one new from the dealers, but they will be very price.
Then there is also possible software changes that need to be made, this is where clutchplate's advice would be really helpful as he has worked with this kind of thing before.
What is the current condition of your gearbox? If it is still good then you are actually in a good position as you have time to source everything do all the needed research so that you have everything ready for when you do the conversion.
This kind of work is of course not for the faint hearted and you would have to decide whether it will be worth it for you, for instance if you are planning on only driving the car for say two or so year then move on then it probably won't be worth it.
Oh and you might also want to chat to Uber sodat or Leonard (the dent doctor) as they could also help you with the technical aspects as both of them have als done auto to manual swaps before, albeit on e34's.