Welcome to CT!
Damn ...
Another rare SR bites the dust - even more rare than most because of the StepSide bed.
It's been a long time since anyone posted about getting attacked by the Taco Curse (getting rear-ended, which seems to be a curse with older Tacomas).
Are you OK? That's the most important thing.
As to your questions ...
No - Toyota did not offer any factory leather seats option on SR's. The leather trim you mention was added after the factory. It might have been done at the dealership as a dealer option or accessory item.
I don't see the door window etching you mentioned. Any 'S-Runner' name etched into the door windows is not factory. No 2001-2004 Taco came from the factory with a model name etched into the glass.
If I see what I think I'm seeing in the photos - small Toyota emblems etched into the lower center area of the XtraCab quarter windows ... No, those are definitely not factory either.
Factory tinted glass was standard.
'Sport Package' was the factory designation for the accessory / trim package specific to an S-Runner. It wasn't a separate package added to an SR. In other words, a 2001 or 2002 SR had a factory 'Sport Package' by definition.
I'm sorry for your loss.