Hi Greg,
Yes, that a new cell limit of the new sheets, nothing to do with FormEmailer there. But I see your point, the cell that has more than 50000 chars is where FormEmailer store its settings.
It's surely possible to change it to save the settings elsewhere or spread it in multiple cells, but it's not that straightforward to code it.
I think an easy workaround you can try is write the major part of your email body (e.g. a long plain text section) in a cell in row 2, as a formula, then have FormEmailer use it as a placeholder, like any other column. And set the formulas location parameter to copy it down and possibly change the closure mode to "clear" just so there isn't a lot of repeated cells in your sheet.
Please take a look on these other questions to see how to use the formulas location parameter: