Our current approach is a database migration (small version upgrade via datapump export and import - 126.96.36.199 to 188.8.131.52), followed by an apps tier migration. All while the production application services are down to prevent user interaction.
Are you doing the platform migration of EBS DB / Application? if not then you don't need to do export / import and it will save your time.
What is the risk of running pre-clone scripts on the source environment during a prior weekend
There is no risk in running pre-clone on source instance; it's safe and you can run online.
The following weekend, we would migrate the database and then bring up the already copied application tier after running the post-copy rapid clone steps.
This should be ok if you are not applying any patches after application copy.
To add to what has been said already, you might only need to copy the concurrent log and output files generated after you copied the application tier.
It depends on your policy for how long to retain the files.