Free space after removing ibdata1 file
It will not answer your question directly, but I wanted to notice you about this ibdata issue in general. Unfortunately, there is no magic solution to decrease the ibdata file size... It is the central point of the InnoDB engine, removing it (even when database is shutdown properly) will cause data inconsistency/corruption. 

The only way to restart from a healthy state (with a small ibdata) is to reinstall a brand new MySQL instance and load the data from your origin, and PLEASE use innodb_file_per_table to avoid having all you data in one single file (MySQL doc here).

To load you current data into your new instance, you can use mysqldump if your dataset is small (few GB) or use "Transporting tablespace" procedures to cleanly import table by table your dataset (example on Percona Blog here).

You can also read this article form Percona Blog which explain many things regarding these ibdata issues.

Max.