When you clone the Oracle Apps system, you only need to run setup_clean. It will clean out topology information or APPS/EBS connection information from the system.
If you do not want any printer setup info, log/out info or profile info carried from source on the target clones system, then please execute target_clean.
When I refresh, I run Exec fnd_conc_clone.setup_clean; and then run RDBMS autoconfig ($OH/appsutil) and then autoconfig on the apps node. Thereafter all the topology information will be populated. When I refresh, I take a backup of target context file, tns ifile, sqlnet ifile. It is safe not to have any information of PROD in the FND tables.
For number 3, you need to backup FND_NODES.
is there any effect on scheduled concurrent requests either on newly cloned or existing test instance after running either setup_clean or target_clean
No, there would be no effect.
As long as you have you standard manager up and running you will be having no problems running concurrent request/programs (assuming other supportive DB and application components are working fine )