I can't say I've seen anyone that has done this successfully yet. I'd love to know if you do come up with a solutions. I removed mine and would love to put something back on since I live on a dirt road.

Yeah. I figured it's been years since people have upgraded their brakes in someway shape and form. But if someone has insight from their own pursuit and wanted to share, this would be the place. I'll list the part numbers here:

Meant for X-Runner:
47781-04030
47782-04030

Other trims, also listing X-Runner:
47781-04050
47782-04050

14WA conversion:
47781-60140
47782-60140

So to reiterate and clarify in case it wasn't 100% clear in the OP, the basic premise is that all trims of Tacomas are listed for both L/R part numbers under both variants of the dust covers. Which leads me to believe that the 4-bolt mounting pattern between the Tacomas is the same whether 5-lug or 6-lug. For the 6-lug guys, there's a brake upgrade guide to use the 14WA calipers and the dust covers from the 4 Runner. If the new and bigger dust covers mount directly on the hub for the 6-lug, it means it has the same 4-bolt mounting pattern. This should mean that it also fits the X-Runner.

The TRD brakes came with 332x32mm 2pc rotors and the 14WA conversion for the 6-lug uses 338x32mm. Therefore, the dust cover definitely does clear in diameter. Again, the concern here is the offset difference between the original (X) and converted (14WA) hubs. The dust covers aren't really that expensive. I believe the 4 Runner dust covers run somewhere around $62 each. The pain here would be to separate the hub from the spindle to add these on for fitting. I don't have the TRD/StopTech BBK so there's no way for me to test. If I could get my hands on a set of the TRDs, I'd definitely be trying this. Or if someone's due for a brake job soon and would like to try and contribute here, I think it'll be a good resource for those that want to add the factory designed components back on.

The instruction manual for the StopTech kit says to:
Trim, bend or remove the O.E. rotor rock shield.
https://drive.google.com/file/d/0B_Kt2Q_-iRXpelFDanhZLXRnMmM/view

Yeah, I've already seen that. The reason Toyota, or any manufacturer, would say that is because they're not wanting to pay technician labor hours past what is absolutely necessary. Especially here because to change it, you have to separate the hub from the spindle and that takes a LOT more time than simply cutting it off.

Edit: thought that was the TSB instructions. This is SOS. They say that because, again, it's easier than finding the correct dust shield or custom fabbing one.