Doing a platform change/Database migration AND an upgrade at the same time can be done in one step. Its not completely recommended - since you're making two large changes at the same time - but its completely possible, and I've migrated several companies from AS/400 to SQL Server while in the midst of an upgrade. We call these "sandbox" upgrades - since the new environment is separated from the existing environment - but its imperative to test thoroughly.
I've mentioned this before, the biggest issue isn't realistically the platform change, or necessarily the upgrade - but when you switch platforms, any third party process that is hardcoded to work on the AS/400 will be affected and needs to be re-coded to work on the new platform. JDE works wonderfully on any of the supported platforms - but the same cannot always be said of other applications !
As for the migration of data - certainly using R98403 is painfully slow - copying a large F0911 will take forever on a single-threaded Table Conversion - but using native database tools, especially going from AS/400 to SQL, will result in data corruption unless you are VERY VERY careful. It will take a LONG LONG time to identify all the different value changes between AS/400 and SQL Server.
However, there IS a way to utilize OneWorld/E1 - to use the built-in data dictionary - and to copy data as FAST as the database can write the data. I've copied across 100,000,000 row F0911's between remote locations between AS400 and Oracle in just a few hours - realistically you can actually create a process that will copy all your data in whatever realistic window you might have.
Of course, I don't just give out this information for free (it is my livelihood, after all) - but I'd gladly discuss this process with you offline. Send me a PM and we can chat.
Remember, you can spend MONTHS trying to develop external 3rd party tools outside of OneWorld - or you can spend DAYS waiting for processes like R98403 - but it only takes HOURS for a professional consultant to migrate data between platforms and create a valid and successful upgrade.