Thanks to everyone who replied. As a forester, and not an electrical engineer, I have no idea what most of you are trying to say, and my lionel repairman does not know how to improve the performance of the 763's or the Niagaras.
To recap:
The wiring to the track is correct. The bell sounds with the bell button and the whistle sounds when the whistle lever is pushed on my ZW-C 180W. I learned how to wire bells and whistles using my old TW. The common ground on the 990 Legacy base was wired to the outside rail. I checked all of this before starting this thread.
Even before I discovered that it caused my locomotives to overheat, the 990 remote was confusing and it limited the top speed of my locomotives. (Yes, my locomotives ran faster using the transformer and slower using the remote.) The only things I liked about the 990 remote was that it really increased the smoke output and made the whistles a little louder. I should also mention that the 990 controller's performance was erratic: sometimes a locomotive would respond to a command, but often it wouldn't.
The ZW-C transformer with 180W power packs is new. The 700e's, Mohawk, Commodore Vanderbilt, Veranda, and S3 4-8-4 all fly around the track. One of the Niagaras did too, when it worked.
All but one of the locomotives, a 763, are new. I am the only person to run them other than the Lionel repairman. All locomotives have been greased and oiled, so friction is not the problem. True, the electronics may be 20+ years old, but the 763's still run, although really slow and they barely pull anything, even after replacing the grease and installing traction tires. I'm convinced that the TMCC boards are sucking the life out of the 763's, I just want to know how to remove them and retain the lights, smoke, and sounds.
I re-oiled the Commodore Vanderbilt and 763's. The CV is now faster than my 700e's and Mohawk, but still not as fast as the Veranda, which is the fastest, strongest, and heaviest (12 lbs.) Lionel locomotive I've ever seen. The CV, although fast, can only pull about 10 of K-Line's die-cast box cars at once. (The Veranda will pull all 15 of my die-cast box cars plus another 8 die-cast coal hoppers.) So that only leaves the 763's, which showed no improvement after oiling, as candidates for a TMCC-ectomy or the eBay scrapyard.
Speaking of the scrapyard, I got word back from Lionel today. There is no fix for the problematic CCII NYC Niagara driveshaft. What's the point of celebrating a century of Lionel with an engine that looks good, but doesn't run? If I want a locomotive that doesn't move, I'll buy one from Hallmark. Lionel had over a decade to fix this problem and their only solution is to recommend that I replace the failed part with the same part. Lionel LLC's apathy is just staggering.
Since my first run of each engine using the new 990 Legacy controller, which resulted in every engine overheating, I have kept the 990 in its box and run everything conventionally. I tested the S3 4-8-4 using an older Legacy controller and a ZW-L, at my Lionel dealer, and there were no overheating issues, so I'm convinced that the 990 controller is doing something to make the locomotives overheat, and considering how little these new 990 controllers are selling for, the word must be getting out. Lionel suggested that the ZW-C may not be compatible with the 990 and their solution was to upgrade to the ZW-L. I believe that the 990 is a poorly designed and defective product and see no reason to spend another $900 for the ZW-L to see if I can get the $300-legacy controller to work. Someone suggested downgrading to a TMCC cab-1 remote, which is starting to sound really appealing, although some of my locomotives are equipped with Odyssey and I was warned by my Lionel dealer that TMCC cab-1 remotes do not work well with Odyssey-equipped locomotives.
At this point, the solution seems straightforward. Sell or trade in my 990 remote and run all of my Lionel locomotives conventionally. Barring any real solutions for the 763's and Niagaras, sell those as well, since they will always break down or run poorly. Finally, I will be very careful about buying any more Lionel locomotives. If I really need to run in a command environment, I'll start over using an MTH transformer, MTH controller, and MTH locomotives, which will happen just as soon as I win the lottery.
If anyone can tell me how to remove the TMCC from the 763s or really fix the driveshaft on a Lionel CCII Niagara, I am still listening. However, I have decided that I will no longer try to make TMCC/Legacy work. Good luck to everyone who still believes in TMCC/Legacy, I'm glad you found a way to make it work and I hope it doesn't ruin your locomotives.