Hi, ROTM,
I would fit the seat further back, its end right in the rear axle vertical and lift your rear set to make room for the standard exhaust pipe. As high as you can where you can still shift/brake. This will allow your knees to be at quite an angle for a touch of ""allowed"" streamlining.
For a 350cc, you can look up at exhaust length pipe calcs on the web, but part of the calcs is dependent on your cam timing, the exhaust opening phase angle before BDC. Contrary to general belief, the higher the better, nearly all 4 stroke race bikes have more than 90 degrees there and some more than 110 degrees.
Then your max revs obviously.
As a rule of thumb, for a 350/400cc, 1"1/2 ID pipe, about 36" long from valve head to end of pipe.
30 to 45 degrees slash cut at the end of the straight pipe will act as very small megaphone, make a nicer noise and slightly improve your torque curve. Since you're probably like me with minimum funds, gear box new set is out of the question, so, yes, power at top is important, but good torque will help you be able to gear the bike higher via rear sprockets.
I don't know if the inner dimms are that common between MAC and Viper/Venom/Thruxton, but if yes, a look at their camshafts/followers will be an eye opener!!!
Patrick