No need to go to archived data. The new GeoTIFFs are just fine. TransDEM will open them out of the box. And you get bigger chunks, too. One new GeoTIFF covers the same area as 16(!) of the older CDED downloads (and, furthermore, each CDED DEM was split into two separate files.) If you still need to stitch two or more of those larger GeoTIFF DEMs together, with the latest TransDEM version you can select multiple (adjacent) files when opening a DEM, and TransDEM will merge them all (provided your machine has enough memory).
The Canadian map indexing system hasn't changed. For the pre-packaged data you always needed the index. Until recently, you had to download an index map. Nowadays they provide it as KML/KMZ vector overlay, but the information is still the same. For the GeoTIFFs you only need the 250k index, not the 50k index any longer.
For example, Kamloops, BC, lies in map sheet 092I in the 250k index and in sheet 092I09 in the 50k index.