The dowels are in the exact same orientation as the bolts. So the direction you pulled the bolts out is the direction you need to pry (basically straight away from the trans). Any lateral movement will only make it want to bind up worse.
As for how to pry it off with the exhaust in place, have you removed the airbox? You gain a ton of room doing that and could get all kinds of stuff in from the drivers side end.
It's hard to tell you what tool to use since I don't know what your options are. I'd probably start with my 18" straight bar sitting where the airbox is, or I've got a 30" with a 90* on the end that extends a couple inches. I'd hook that under the starter and run the bar straight out of the engine bay.
If you're really worried about the exhaust, you could just take it off. No doubt it would give a ton more room and it's not that hard to remove. Just depends if you want to spend the extra time.
Last edited by bumpin96monte; 12-20-2016 at 10:32 PM.