I assume you're using IR pass filters here to block the visual spectrum.
The white balance range in Lightroom stops short of fully balancing an IR shot. You can force the white balance by pushing shadow/highlights towards green also.
But there's actually no need to fully balance if you have Photoshop or any other application where you can separate individual channels. The intense magenta cast is an artifact and there's no "color" information in the IR range, it's perfectly monochrome once you get it balanced. The Bayer filter dyes have different transmittance levels to the narrow IR spectral range, but it's just a difference in overall gain.
Unfortunately the green dye has the lowest IR transmittance (causing the magenta cast) - while the Bayer filtering is biased towards green 2:1:1, so for IR it pays to give as much exposure as possible to compensate for this.
How was the camera modification done btw?
Normally only the IR/UV "hot mirror" filter is removed, but the Bayer filtering remains. The problem with that is that the dyes behave differently in visual light vs. IR or UV. You'd think IR wavelengths were primarily recorded by the red-sensitive pixels, but in reality the blue-sensitive pixels are almost as sensitive to IR.
UV contamination is also a consideration. Most filters were originally made for film, which had different spectral characteristics.
I don't know if it's possible to replace the Bayer filtering with something more appropriate for "extra-visual" sensitivity, but that would of course be a non-reversible modification rendering the sensor incapable of normal color work.
Other than that, "IR color" imagery is only possible by allowing some visual wavelengths, or through "IR false color" procedures based on multiple exposures and then swapping channels.
Sorry...I don't think I explained myself well.......When the Images are loaded into Aperture, they appear exactly as shot with the correct WB that has been built into the IR converted 5D.
However, when they are loaded into Lightroom CC, it cannot cope with the WB range and gives it a very Red hue.
I have loaded the DNG Profiler and adjusted the Temperature range, but the image is still nowhere near as accurate as the one that loads into Aperture.
What can I do in Lightroom to cope with this please ?
As I said (perhaps not very clearly), you can push Split Toning shadows + highlights to extend the range.
But my other point was that IR is a moving target and there are many different varieties, each with different requirements. If "pure" IR with no visual wavelengths, there is no color information there and you can just dial saturation all the way down to get a white-balanced result.
Can you show an example?
Yes, Lightroom has a fairly limited white balance range, and here the "tint" slider clearly stops short at the green end. The Lightroom version has massive red channel clipping.
But you can extend the range by using Split Toning:
The trick, of course, is to hit the exact hue to compensate with - OTOH realism doesn't apply here anyway. The main thing is to avoid channel clipping, and then you can do final adjustments from there.
I suspect the best solution to this is a custom camera profile, but that's above my pay grade in this case. Obviously you can't use a color checker to make it.
For simple white balancing, however, you can use sheets of tetrafluoroethylene, aka Teflon. It has equal reflectance across all wavelengths from deep IR into high UV. Teflon is available in white and medium gray.
I would strongly suggest that in this case there is no such thing as a "correct" rendering. There's no particular reason to take Aperture - or even the camera - at face value. IR is a moving target simply by virtue of being non-visual, so there is by definition no "standard". The best you can hope for is a standardized procedure, so that results are reproducible under the given circumstances.