I can not find this particular prayer in any of my prayer books, nor in the Raccolta, but it seems orthodox. It is important to remember that you can pray in any way you want. Variations of particular prayers are common and, in most cases, harmless. If it settles your conscience to omit the bolded section, then omit it. 

Is it okay to say this version of the St. Gertrude the Great Prayer?

Eternal Father, I offer Thee the Most Precious Blood of Thy Divine Son, Jesus, in union with the masses said throughout the world today, for all the holy souls in purgatory, for sinners everywhere, for sinners in the universal church, those in my own home and within my family. Amen.

It seems the last part was added later on, if I had learned that correctly years ago.

I understand that the promise of one thousand souls being released was prohibited by the Church, but it seems the prayer itself in the above would still be alright to say, even though the last part is not given in Read Me or Rue It of Fr. Paul O'Sullivan, O.P. as officially approved by a real Portuguese prelate.

It is so hard to find the correct information on this. One cannot be too careful when doing research on such things as devotions and whether or not the Church has approved them or has not at least condemned them and reasonably are

I pray this prayer and yes, the ending was added, but the original prayer is still intact at it's beginning. It is nice to think that 1000 souls are released eveytime its said and St Gertrude is so powerful, but no guarantees here. I still pray it every day and occaisionally say 50 on the Rosary beads as there is a chaplet for this prayer as well.