Thanks Lorraine for your inputs. Given that it was my first post, I had to be brief in my earlier post.
We have been meticulously pouring into the mysql slow query log and compared with our earlier slow queries and there are many queries which are indeed slow in the order of 20-80seconds. But all these slow queries were there even before migration and thankfully we do not see any new hits there. Also indexes look ok and we did add 2 indexes to 2 our huge tables which helped a bit.
Our ibdata1 file size used to be 5 GB which has since the migration has grown to about 14 GB. Should this be a cause of concern ? Can you please suggest some tools that can be run immediately on the database to check for data integrity and to check if innodb internals look healthy.
Once again thanks for your response and do ask if you need any more metrics.