Any time you change a component of a stock engine to improve performance or economy of its operation you normally change the operating range of peak torque and peak HP, that being said do you want more power or not?
If so you can use the stock heads and intake with the slightly bigger carb and a stock type cam and slightly improve the motor performance from idle to peak power with that carb
If you increase the stroke a little bit to 3.91 or up it to 4.250 stroke and leave everything else the same the increased stroke will improve the motors performance by a little or a lot depending on which stroke you choose
I really like making and driving stroker motors on the street and at the strip, I like more power a lot
If money is not a real problem look at increasing the stroke to 4.250 with a good balance kit from a good company or buy the individual components and have it built and balanced locally the way you want it
Be careful on the final true final compression ratio with any iron heads, stock or modified I like and shoot for 9.5 to 1 or lower on my iron headed street and strip builds
Good luck either way