Yes; TTT was broadcast in HD. If you do not have the original broadcast I suggest you join newsgroups and download that rather than working from an encode.

The Blu-rays have their problems, but the DNR and EE mainly affects the FOTR. TTT and ROTK are not too bad, and have better overall picture quality than the HDTV captures, which, though good, have problems of their own. Bill Hunt offers a balanced perspective on the issue.

http://www.thedigitalbits.com/reviewshd/bdreviews032310.html#lor

I recommend using the Blu-rays as your main source and adding in the HD scenes from the EE of the TTT. For ROTK, you will have to upscale the PAL DVDs, as you have said, or be patient and wait for the EE Blu-rays to come out.