I doubt that ballasting the track caused the problem. Somewhere, there's some crossed wiring or a failed component.
First thing I'd do is disconnect all of the transformers, DCS, TMCC, signals, etc. and remove all engines from the track. If you have any block toggles, turn them all off. Put power to the track from one transformer, turn one block on, then try to run one engine in conventional mode. Advance one block at a time until you can run reliably over the entire layout. Then add back one thing at a time and fully test it. Eventually, you'll add something and the problem will reappear.
I'm also confused by the statement "installing block sections to accommodate my MTH trains". What does this consist of?
