As it turns out, I tried a different counterweight for the tonearm, and all is well. Pro-ject makes 10 different counterweights for this TT! Each has a range of cartridge weights that can be used. Don't ask me, it wasn't my idea. So, now that I have the correct counterbalance, and Rebalanced the tonearm, the differences are great. What a little nightmare that was. Besides not tracking correctly, the original set up had too much bass, and generally didn't sound very good. Of course, it couldn't, given the circumstance. Now, that I have things right, the sound is getting better but I have ordered a replacement stylus that will be here next Monday.
I was also able to get a new phono pre from Vincent Audio, and that helped a bit but not as much as I would have hoped. All is not lost since eventually the parts for the phono pre that I am building will arrive and we will give it all another go. I just know that this set up is able to do very much more, but you have to al least give it a chance with better equipment to start with (and correct alignment and etc!).