I had two allergic reactions to benzoyl peroxide around a year ago (I was using 10%).
My acne has been pissing me off so much lately that I decided to buy the products for the regimen.
I had my first trial last night, followed instructions perfectly. Though 12 hours on and this morning my skin is itching/burning/red and just irritating like hell.
Should I stop using or power on through it?
Sounds like you have sensitive skin, and for some people severe redness is not uncommon. So hopefully you can just power through it, but I would stick with a pea-sized amount until you're sure you're not allergic. Here's a link to the Regimen FAQ and what they recommend.
http://www.acne.org/regimen-help.html
Read the first 4 FAQs on doing the Acne.Org Regimen. I highly recommend the Regimen and hope you can be successful with it! 
However, if you experience blistering, crusting, or swelling, I would stop using the treatment.
I agree with D ^
You may have been so irritated before because it was 10%. A concentration that high is bound to irritate most people. If it was a true allergic reaction to the BP on the other hand, you'll be allergic to the 2.5% aswell.
As Deb said above, if it's blistering, crusting, or swelling that's an allergy. But if it's the redness, itching, and dryness that you're experiencing as mentioned in the FAQs, that is something that does go away with time once your skin adjusts to the treatment.
You just need to be sure to start really slow and use your best judgement in regards to what your skin is telling you. Some irritation is definitely normal, but if something really doesn't feel right despite the adjustment side effects, then don't continue using it.