[Lava]

DarkZephyr 

1. In the cut scene with Yoshimo and Irenicus at Spellhold, he does refer to my PC as a "she". He talks about letting "her" go and such.

That certainly must be changed! will look for those lines and make sure he can properly recognize you.

2. About the smashed heart.  Does that mean I cannot take the heart to the temple of Ilmater?

Yep, Irenicus and Bodhi realized what's going on and wanted to play on your feelings... however, that's not the end of the romance! The lack of the Ilmater plot does not mean there's no other story to fill that gap! It's also best to have Imoen in your team, but that's not a must, so don't worry if you replaced her with someone else.

Oh, and I'll edit your post to mark the spoiler. Thanks for all your feedback