Two different things that might be causing issues here:
“sample-id” in the first line should not be capitalized
it looks like your file contains windows-style line breaks, which could be causing the issue. If fixing “sample-id” does not fix things, try opening up your file in a text editor to replace the line breaks.
That is a different error from what you reported above — in this case, QIIME 2 can’t find the file! It looks like you are running that command from within the wrong directory (in the original error you gave above, it looks like your current working directory was paired-end-sequences. Either change into that directory or use an absolute path for that file to make sure QIIME 2 is looking in the right place.
A little confused on your response; it was one of the same issues I'd reported before: two failed attempts in one post. One was the same as what I posted last, except that before, I posted the 2018.6 result with a source-format; I had tried 2018.8 with input-format for the later one, and did that again above. Those weren’t the problem, but --input-path. Both had the same results - no file found.
The manifest file is in the paired-end directory, though I copied it to other locations after the error appeared.
In this case, it looks like the file ManifestRun2.csv doesn’t exist in the folder that your terminal is currently working in. As @Nicholas_Bokulich mentioned, you can change working directories, or specify absolute filepaths. I just want to point out that this is the same “type” of error as before - previously you ran into issues because you left off the end of the file’s name, while this time, you are running into a problem because you are missing the leading part of the file’s name (in this case, the path to the file). To paraphrase @ebolyen - computers are very naive, you have to be exceptionally explicit when telling them what to do, in this case, you need to take care to provide precise filenames.
Thanks for being patient here, I know these kind of general computing errors can be frustrating, but we will get through it together!