Are you sure it's an R5? The L2D models are several years old, so they did not have the R5 XP-G in them... Unless you modified the light with this newer, more efficient emitter.
I think you mean Q5 XR-E. When you look at the LED, is the dome about 3-5mm across, with a metal ring around its base? If so, you have an XR-E based light.
It is very possible you may have damaged the LED by running it in Turbo mode for long periods of time. Excess heat may have built up in the head, especially if you didn't hold it by the head while running it in turbo, to allow your circulatory system to cool the light.
Unfortunately, the new LD model heads have a different type of threading on them, more trapezoidal, like the Quark line-up, not the triangular threading of the older models. So, no, a newer head will not work with your L2D battery tube.
You mention you use alkalines all the time... Now, I'm not sure what current is drawn from the batteries to produce about 180 lumens, but alkalines could not provide anywhere near that current for long... Ni-MH and Lithium AA's, yes; alkaline AA's, no. The internal resistance of the alkaline cell would cause the voltage and current drain to drop rapidly, greatly reducing run time on Turbo, and making it bright for a few minutes, then dropping out of regulation, and dimming gradually over a period of time...
With this last statement, it makes it seem less likely to me that you could have damaged your light with heat, for he above reasons... It may still be the case, but it seems much less likely to me.
The L2 models were a lot floodier than the newer LD models... Two questions: What light were you comparing output with, and how did you compare output?
If you were comparing output by looking at the hotspot intensity, that may be the reason the light appears so dim. Hot spot intensity will _never_ be able to tell you a difference in output between two lights. Here's why: you're comparing lux (the concentration of light), not lumens (the total amount of light). A good analogy would be a mini-mag AA, and a laser.
The laser appears brighter, because it's "hot-spot" is so tightly focused. However, while it has a lot of lux, it may only produce a few lumens. The opposite is true with the mini-Mag. It doesn't appear so bright next to the laser, because its total number of lumens isn't as concentrated. The light beats the laser in total output, but not in throw.
To more accurately compare outputs, you need to do what's called a "ceiling bounce test." Basically, you go into a dark room with your lights. Point them at the ceiling(from the same height) and turn them on. Look around the room to see how well things are illuminated. Then switch back and forth.
At this point, no, I don't think Fenix will be able to help you. They have a two year warranty on their lights, but at this point that warranty is probably run out.
While the LED may be cooked, the driver probably isn't. You could swap in a new LED if you wanted to.