tools to reconcile experimental transcripts with reference annotation
I've never tried this myself, so I don't know how easy this is...

One option would be to start with GMAP, which is meant to align whole transcripts against the genome. The really nice thing about this is that it can directly produce GFF3 files. You can then use that with your Ensembl GTF with cuffcompare or whatever the equivalent is in stringTie. You should then be able to get the information you want from the transfrag codes.