I resolved the CLEANMARKER issue by using the -n switch for mkfs.jffs2. However, I have not resolved the "Empty flash" issue. I'm not too concerned about it at this time.
I did get another error message when using nandwrite to write output obtained from nanddump. I noticed that the default behavior for nanddump is to include oob data, while the default behavior for nandwrite is to assume the input file has no oob data. So you'll have to use the -o switch on either utility to get them behaving the same.
I've generated my images of the original device's flash and will probably test out writing it to other devices today.
Honestly, I've never had an issue with the tar process, but I only had to untar on the original device. The clones just get the raw flash contents. I assume you're using the script on the how-to. I've never had a problem fitting the rootfs into mtd4 (249.5 MB), nor get "No space left on device" errors. Is there any other info you can provide?