I assume that you understand that TransDEM uses DEM (Digital Elevation Model) files for the terrain and then overlays maps (topo or otherwise) on top of the terrain. It sounds like you've already been using SRTM files for DEMs. So some of what I've written may not be useful. The USGS web pages and links can certainly lead one on a wild goose chase.
For DEMs (terrain files) and GeoPDFs (2D map files) I often use the USGS's The National Map downloader client at:
https://apps.nationalmap.gov/downloader/#/
It takes a while to get used to the interface. The TNM downloader link is useful if you are looking for higher resolution DEMs. SRTM files have a 30 meter resolution and you can get higher resolution DEMs from the link listed.
A few days ago, the above link wasn't working and I did a web search for "SRTM data" to find an immediate source while the USGS site was down. I don't remember which one I used, but I didn't bother with any site that requires registration. I replaced the SRTM files with higher resolution DEMs after the above link was working again.
It is also useful to configure TransDEM's "Map Tile Server" feature found under the Raster Map tab instead of using topo maps for the 2D maps. (See TransDEM's user manual.)
The GeoPDF topo maps sometimes have a small offset which may need additional work to fix. I believe that TransDEM's creator wrote that it expects GeoPDFs to use the NAD 27 format rather than the NAD 84 format that many GeoPDFs actually have. (I may be remembering the wrong numbers.) He recommends using the Map Tile Server feature instead for the 2D and topo maps. The map tiles should not have offsets.
Each TransDEM user seems to favor various sources for the maps depending on either ease of use or desired map detail.
Hope that helps,