1) the cvds from the tranny are angulated upwards to reach the diffs - bad energy transfer
Answer: Well ALL 4wd vehicles to this...be it up, down or even left and right offset. Even real cars go down to the axles from the transfer case. 1/8th buggies slide the center diff over to get better CG and thats probably the reason in this case as well.

2) the shape of the exhaust pipe seems inadequate
I guess this is an odd thing to point out, but that header and pipe style are the same used on a 1/8th buggy...so you could probably upgrade fast.

3) the tie rods of the steering linkage are not parallel to the cvds
Very common really, plus the angle allows for ackerman and reduced bump steer.