You write
1) “Earlier Developer to me have migrated MS-SQL2008 Database into MYSQL using 2 tools MYSQL Migration tool kit for Data and SQL ways for objects(Stored Procedures…)”. “MYSQL Migration tool kit* migtration toolkit has been discontinue several years ago. Additionally we cannot comment on it. it is not our tool. SQLyog/SJA will import table data – it will not even attempt to migrate 'stored programs' of any kind.
2) “At first sight i noticed there are several Issues with SQL queries and procedures in Migrated tables”. Undoubtedly. SQL syntax is not the same in MS SQL server and MySQL. In particular not for “strored programs”. You should expect to spend quite a lot of effort to rewrite Stored Procedures (and Triggers). I don't belive any tool can do it automatically (and I would not trust anyone telling that their tools can).
3) “.I found MonYog tool is the ideal choice, how can i connect MYSQL table query to Manlog (you mena “MONyog” I guess?) and possible solution.”. You could use the Query Analyzer to spot performance issues. Did you read the documentation at http://www.webyog.com/doc/MONyog/Log_Analyzer_introduction.htm (and its subpages) ?