So couple things I would validate, but doesn’t sound like it would be the case. If you do check the Traffic Shaper, you don’t see anything there other than the blank section where the queues would be. You also haven’t setup any limiters but those generally just caps so you wouldn’t get a burst than a drop.
If you login to your pfsense router, run a top while the transfer is going on and make sure you aren’t seeing any high interrupts which might be slowing you down.
Mine jump up a bit when pulling down 500 Mbs, but nothing more than one core out of my 4 can handle. I traffic shape a gigabit link.
If you don’t see anything obvious, I’d go along with your simple route and limit the pieces of gear involved. If you can test just PFsense router with a machine plugged into it, start there and add pieces to your chain till it breaks.
DNS really shouldn’t be an issue as you’d see those in your logs and it only asks for the DNS on the initial connection out. You’d see a clear message saying it can’t lookup a DNS name.
You’d see timeouts too like:
rclone.log:2018/07/25 21:28:52 ERROR : Radarr_Movies/I Feel Pretty (2018)/I Feel Pretty (2018).mkv: ReadFileHandle.Read error: low level retry 1/10: read tcp 192.168.1.30:38943->18.104.22.168:443: i/o timeout
So that’s a retry for a connection which can happen. If you can share the full debug log from start to finish, that might have some info in there too.