I would copy the stock intake out of larger 1/4 thick wall alumiunum tubing. Use 3/8 for the flange and make the log the same size or larger than the charge pipe or turbo outlet.
Throttle body can be on either side use the intercooler to move from one side to the other. Put the turbo low and allow the charge pipe to snake around as needed. Looks like you could run the chargeipe out the turbo and down under to the left side and into the cooler and out the right side and up to the throttle body pointed in some direction that fits with as little angle as possible. Make any 90 degrees right angles at the throttle body and use the silicon 90 to make a smooth bend. Not perfect but will make crap load of power before its an issue. If all the charge pipe is 3" and intake log at 4" with 2" id runners tapering into the port as smooth as possible you should be able to support any hp a normal build up of the bottom end could support. Sometimes i have used thicker wall pipe and ported the shape needed for oval and strang eggplant efi ports.
Hope this helps cant really give anything exact because im not under the hood. But i will tell you crappy charge pipe will still make a boat load of power and can always be cleaned up or hidden. Buy some charge pipe kits with lots of J bends and a hack saw and get to work trying to make it fit then built the last part of the intake and make it all match up.