Just about any header will give you better flow, not sure there is a big difference between any of them for the Samurai.
The biggest restriction in the stock system is the head pipe, between the manifold and the cat converter. It is constricted inside by another pipe that is maybe 1/2 the diameter of the exhaust pipe.
If you know anyone that can fabricate you a cheap 2" exhaust you can use the stock manifold and save you some money.
Dual batteries are a good idea also. A higher output GM alternator would be another good upgrade (also easier/cheaper to find a replacement). Also the jump-boxes are pretty handy too. Used one while out on a trail to jump start and it made it so much easier.