3" exhaust is HUGE for a stock motor.
And will absolutely positively not hurt a damn thing. As long as you've got the right sized header primaries (1 5/8" for a 302) you're in great shape. Ideally you want no more than a 15* outward angle to smooth the transition of exhaust gases in the exhaust tract. So if your collector is 3", then a 3" mid-pipe and cat-back is what the doctor ordered. Even if there's a change from 2.5 to 3" at the collector, I wouldn't worry about it because there's unlikely to be any noticeable change in power or torque at that point.
As mentioned, swap the gears for 4.10s or 3.73s at a minimum. Why do the swap to a lower ratio if you're trying to make a fast car.
Other than that, it sounds like you've already done the basics. If I were you, I'd start building the upper end of the motor with a new set of heads, a cam, and an intake. Supporting mods you'll need include new injectors (Save yourself future hassle and go with 36-42 lbs injectors). In conjunction with the injectors get a larger MAF calibrated to them. The 75mm Pro-M bullet was always a great meter, but I hear a lot of people are going with bigger meters than that, now. I personally recommend Pro-M meters. I've had 3 of them now and all have worked flawlessly for me.
Additionally, a 65-75mm throttle body would be appropriate for such an engine combination. Bigger isn't necessarily better. Find out what the inlet opening size on the aftermarket intake you'll select is, and match the TB to that.
Since you've already mentioned stroking the engine, pick heads that can follow you there. AFR165s are essentially a direct bolt-on with no need to have any work done on the pistons. However, spending 1300 dollars now and then not having a cylinder head that will be efficient when you stroke the motor may be a waste of money. TFS twisted wedge heads, or AFR 185s would be my personal choice for your combination. For the intake, I like the RPM2, and the Systemax 2 intakes. The only cam that will ever go in any of my cars is a custom cam. Ed Curtis has done 2 cams for me and both have worked out very nicely.
With a setup like this, I think you'll make north of 300 rwhp with your 302, and probably around 400 rwhp in a high (for pump gas) compression 347.
Good luck,
Chris