It may feel like it pulls harder in 3rd or fourth, but physics says it pulls hardest in first, then second, then third, then fourth, then fifth. Thats just how it works.
You may only gain 30mph during second gear while you gain 45mph in third (random made up numbers), but second still pulls "harder".
The 2nd-3rd shift is a big one, but if you wind it to the redline in 2nd it still drops you right next to the torque peak when you shift into third, which is roughly correct as far as gearbox design goes.
The thing to remember is that your racing a B16, they have 160hp (compared to your 135-140).
The trick to them, is that they have NO power under 6k, so first gear in a b16 is very very slow, you have to go through 5k before you get any power. Once you do get to 6k, it pulls hard, shifting into second leaves you above the vtec mark(6k), so it keeps pulling hard.
So heres how it works:
Prelude wins first gear, because we have the low end power to get into our powerband way before the civic does, this gives us a car length or two.
Civic wins second gear, but not by enough to pass the prelude, the lude should stil have half a car to a car and a bit at this point. The civic second gear lasts longer then the preludes, also, so the civic gets an extra burst of catch-up-ness when we shift and it's still in 2nd. At this point in time the civic is moving faster, but is still behind.
Now we're to third gear, a much longer pull then first or second.
The civic wins third gear, and more importantly it wins it by a good chunk.
The combination of shifting later, and being at a higher speed going in means that by the end of third gear for the prelude, the civic is only halfway through it's third gear, and going substantially faster.
Fourth gear is a dead loss for the prelude.
TL

R version:
Civic = 160hp with proper gearing for it's powerband and a five year old engine.
Prelude = 135hp with proper gearing for it's powerband, and a seventeen year old engine.
Given roughly even drivers, the Civic wins.