Guide pins are more important when installing than when removing a tranny. They'd keep the input shaft straight going into the clutch and prevent tweaking the clutch disk. There's no reason you couldn't use one of the lower bolt holes (unless they're obstructed as well), but it wouldn't be a stable as a pin in the upper hole. It looks like you could put a short guide pin on the passenger side upper bolt. It would have to be the same length as the space between the bolt hole and the lug behind it to be able to install and remove it.
The problem with using a floor jack is that the tranny is teetering on top of it. Some of the guys have used an engine hoist sticking into the cab with a chain bolted to the tranny. That's a bit more stable as there's no worries about the tranny falling off the jack.
Or you could get out your grinder with cutoff wheel and "fix" that bit on the tranny that's in the way.
