Was wondering what issues I might have doing the swap? I realize that the newer turbo is a larger and more efficient. How should I go about dealing with the electronic wastegate, downpipe etc....

buy a $600 controller ;)

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http://www.competitiondiesel.com/forums/showthread.php?t=48297&highlight=he351VGT

I was speaking of the HE351CW, not the VGT. They are different aren't they?

The downpipe will bolt up, and you can buy a plug from places like ATS, or just leave the solenoid installed and unplugged. They allow air thru when not powered. You will need to adjust the WG, as they open about 22-24 psig. The turbine is the same as your HE341, but the compressor is bigger (and about as big as you can go without severely unbalanced flow).

It's a nice turbo