I think some Asics and New Balance have width fittings. I'd start there. And cut your toe nails!
Worth noting that a lot of trainers seem to come with bigger toe boxes to encourage a 'more natural running style'.
What kind of distances were you doing before this training. I'm inclined to agree that, if you've been running a while, you've just boosted your mileage too early and need to ice and back off a bit. How long til your race? 50 miles?