I know this is an old thread, but I just did the same thing Cracker Shack did, and I wanted to comment here so others can search about it. I bought a PT-6000 to replace my 6004 fiber system. The fiber system lenses screw into dedicated return fittings for the lights. I removed the lenses, then attached a pull wire to the fiber after removing the end fittings on the end of the fiber in the pool.
After that, I pulled the fiber up through the base out of the pool, then attached the treo led lights to the pull wire and brought them through the base.
Wiring is a snap, though I do have a problem with the remote---it doesn't work unless I'm right on top of the podium. I read the troubleshooting guide and found the antenna has a 12 foot cord, so I pulled it out of the podium, but still only works if the remote is a foot from the antenna. Either the antenna or the remote has an issue, and I'll deal with it this week. The lights screw in the same way the old lenses did, and has multiple colored escutcheons to match whatever color fittings you have. Very doable as a DIY project.
To his original question, the instructions say to have the water below the fitting, though the only reason I see this is required is so that you don't leave water in the conduit. It is likely more important in northern climates where water in that conduit could freeze, but here in Louisiana it's not a big deal. I did do the swap while the pool was empty though, taking advantage of the pool being drained by the plaster crew. If I had to do the retrofit with the water in it, I think removing the fiber and attaching pull wire would be very difficult, to the point that I'd consider just pulling the fiber and using a fish tape instead in that scenario. I also applied Teflon tape to the threads of the LEDs, but it doesn't call for it and probably isn't necessary.