Issue after moving the ib_logfile1 and ib_logfile0 files
How are you coming to the conclusion that "these files contain some data even after graceful shutdown"?

Even if it's been fully flushed and uncommitted transactions cleared, etc., by using innodb_fast_shutdown = 0, the "flushing" probably means that the file is "empty" as far as MySQL is concerned, but it won't physically be full of zeroes.

If you start MySQL up again, it will probably zip through the files to the latest Log Sequence Number and realise that there's no more work to be done (someone familiar with the source code that handles the innodb logs would be able to confirm/deny this).

Your steps should be absolutely fine, but I'd take Baron Schwartz's suggestion and move the ib_logfiles somewhere instead of deleting them, just in case it turns out that the server doesn't shut down cleanly for some reason.