In my limited experience since I have gotten back in to photography, in situations where you want to use a prime lens, you probably have fewer time-sensitive concerns that would require the focusing speed of an auto-focus. In addition, you might often be using a prime in low light where a very open aperture and shallow depth-of-field can make auto-focus more challenging to use. I think that in low light and shallow depth, auto-focus can be both a blessing and curse, and whether it is a blessing depends on your camera knowledge and ability to trick the auto-focus into performing to your bidding (e.g. setting your focus by pointing at the subject, depressing half-way to engage focus, then composing your frame the way you want it). For me, using manual focus on my auto-focus 50mm f/1.4 Sigma prime enhances the feeling of control and connectedness with what I am shooting.
I can't say what the story is on converting FD lenses to EF mount. If you can find an adapter that allows you to use the lens but still focus to infinity (i.e. no change in distance to the sensor from the back of the lens) then, bully for you. I think the primary reason for the ascendence of Canon to best-sellerdom in the DSLR world was the quality of their lenses at about the time the conversion from FD to EF mount took place, so you should feel pretty good if you can get the better FD lenses to work on EF cameras.
I think the thing to remember is that, while L lenses are really cool from what I have seen and used, the cost of your very good FD lenses is basically free. That is compelling. If you can get them to work well, that is to be considered, but those lenses won't be best for every situation.
No knock on Nikon intended here. Also, this is just an opinion from a guy who is still learning the digital ropes. I welcome more learned observations.