If you don't want slow to start you need --s3-disable-checksum
Hmm, things to try
Try setting --s3-upload-cutoff 1T (very large) so that you only upload files with single part uploads - does that help?
Also try --s3-concurrency 2
Related threads
I suspect this is caused by some new rate limit at cloudflare - remember R2 is a relatively new service and we've seen quite a few changes in how it works over its brief life.