An opened up exhaust will not give you less torque. It will always give you more torque at some rpm in exchange for a possible loss at other rpms. If you're lucky, and it's a lot better than stock, you get extra torque everywhere.
The question is... at what rpm does that happen? Because if that rpm is too high, then you won't see any benefit from it. With a single cylinder, the most you can do is optimize tube size and try to move that sweet spot around. That pulse-scavenging exhaust looks like the bomb, though I expect the operational range for the scavenging effect will be rather narrow.
Intakes are complicated. WAI makes for better economy but good luck finding warm air in front of the bike! Some filter panels make for better economy in cars by altering MAF sensor readings... which is kind of hit or miss... and I'm not sure whether your bike's EFI is MAF or MAP referenced.
On a bike, re-gearing is the most cost-effective way of ekeing out extra MPG. After that, it's fairings and possibly a windshield (unless you'd like to perfect your tuck...
).