I'm not an Exadata/Exalogic expert but I'm somehow familiar with the steps
Answers to your questions:
Need help for metalink note migration using cloning from AIX temp server to Exastack using transportable tablespaces. Should with this note : Upgrade Guide to 126.96.36.199 on Exadata (Doc ID 1373255.1) enough ?
1. For database migration, please see the following docs.
Migrating an Oracle E-Business Suite Database to Oracle Exadata Database Machine (Doc ID 1133355.1)
Oracle E-Business Suite on Exadata Resources (Doc ID 1512711.1)
Oracle E-Business Suite Release 11i & R12 Patches Required with Oracle Database 11g Release 2 (11.2.0) on Exadata (Doc ID 1392527.1)
Some other interesting MOS docs.
Exadata Database Machine and Exadata Storage Server Supported Versions (Doc ID 888828.1)
Exadata Critical Issues (Doc ID 1270094.1)
If unpredictable event for example (I don't wish this), user needs to make existing production goes to online till EBS on ExaStack ready with 1 old week data, should I use golden gate to sync data with already ebs-deployed on ExaStack or (ask for another downtime and use transportable tablespace again) ?
2. Please see (Doc ID 1133355.1) referenced above.
Since EBS 12.1.3 still using OC4J, how the way I autoconfig Apps Tier after post-clone on Exalogic ? still using common post-clone ?
3. Yes -- Please see "Migrating the Oracle E-Business Suite Application Tier using Rapid Clone" section in (Deploying Oracle E-Business Suite on Oracle Exalogic Elastic Cloud and Oracle Exadata Database Machine (Doc ID 1460742.1) ).
If you are on 188.8.131.52 with 184.108.40.206 then you can follow any of the Paths mentioned for "220.127.116.11 with 9.2.0.x or 10.1.0.x database" -- Path A or Path B or Path C. I would recommend Path C since it will take you directly to 18.104.22.168/22.214.171.124
Please note that direct upgrade to the new Oracle Database 11g release is supported from 126.96.36.199 or higher, 10.1.0.5 or higher, 10.2.0.2 or higher, and 188.8.131.52 or higher -- Preparing to Upgrade Oracle Database
If you are on 184.108.40.206 then you need to upgrade to 220.127.116.11 first -- Oracle Applications Release 11i with Oracle9i Release 2 (9.2.0) (Doc ID 216550.1)