My research led to a wonderful free (donations will unlock additional features) software package called Raw Photo Processor - caveat is that it is Mac only, which is not an issue for me. Now this convertor keeps the RAW files as neutral as possible, so much so that they look very "cool" in comparison to other converted RAW files from other convertors. I almost feel that they need a slight warm tone added to mimic what I see with my eyes.
I also found a minor modification to make to Lightroom to correct the unexpected and unwanted modification to my files on importing. Under the Camera Calibration section of the Develop Module, change the profile to "Camera Neutral" to minimize any automatic processing and/or changes from what your camera captured.
As I move forward, I will most likely move away from using Lightroom and Photoshop as my primary software for creating HDR images. Photomatix, while not perfect, is the most popular program for producing HDR images and tonemapping them and my testing/trials of it have confirmed that I will be getting a full version. Now Lightroom is my primary cataloging and processing software so it will be staying as part of my workflow, especially now I've minimized it's interference with my RAW files. I will likely keep using it to feed RAW's to Photomatix, although I'm seriously thinking of making a donation to RPP to unlock all the features and continuing to evaluate it against Lightroom to get the most neutral files to produce HDR's from.
I'll also continue reading the HDRI Handbook 2.0 from the people over at HDRLabs. If you are really interested in learning about the technical aspect of creating HDR images, it is a very good read. The website is also a very good resource that I recommend checking out.
As a visual representation of how my technique is evolving, I thought it would be interesting to post some comparison samples of one of my images so you can see how much things have changed.
From left to right you can see the progression from my original HDR image, through to my latest version (still using Lightroom and Photoshop to merge and tonemap). Certainly some significant improvement in the overall look.