Sounds like a mild combination. The engine/tranmission has to work as a system, so you need to match the parts. To assist the 2-speed gearing (with a stock long block 350) you should focus on improving mid-range torque.

Air in:
Four barrel manifold and small four barrel carburetor (450-600 cfm squarebore or maximum 650 cfm spreadbore). Don't waste your time with adapting a 4bbl carb to a 2bbl manifold or vise-versa. Edelbrock Performer intakes can easliy be found used. Pick a carburetor brand that you are most comfortable with tuning. Make sure the secondaries are vacuum actuated, not a mechanical linkage.

Air out:
Dual exhuast will help even with stock manifolds. No more than 2.25" is necessary with this mild combination. An H-pipe or X-over pipe will assist in torque. If you go headers, use the smaller primaries (1 5/8"). Ram Air manifolds would be great for this combination.

Optimize ignition timing:
Try advancing your distributor in 2 degree increments. Keep doing this while listening for detonation during acceleration. When you start to hear detonation or performance drops off, retard it to the last ping-free setting. Using electronic conversion kits will reduce variation from points wear. Crane sells a unit with a rev limiter for less than $100. Good insurance for stopping disaster.

Final note, changing the gearing will improve off the line performance, but fuel economy will get worse and the higher revs on the highway will be both annoying and increase engine wear.

Swapping the trans might be something you didn't want to consider, but it would make a big difference. Since you have a mild engine, you could probably get away with a stock rebuilt 2004-r. You'll have a better off-line acceleration gear as well as an additional economy gear. Any more mods and you'll need to have a 2004-r specially built.