They have supplied you with the kit that is used for 1hz after market turbo, not factory turbo. I don't think denco even make a casting for that barrel intercooler to factory turbo.
Most ater market turbo kits for 1hz motors have the turbo outlet pointing pretty much vertically up. The factory turbo outlet is angled towards the engine.
To rotate the compressor housing on the toyota CT26 turbo to a different position is not an easy task. First you will need to remove the turbo.
The biggest problem is that the wastegate actuator is mounted on the compressor housing so by repositioning the housing, the wastegate actuator rod will be out of alignment, this may change boost control (these wastegate actuators are NOT adjustable) & you will need to reshape the rod to get the correct alignment. Another option is to fit a different adjustable wastegate actuator.
To rotate the housing there is an alignment pin on the turbo body and alignment hole in the compressor housing. You will need to drill another alignment hole in the compressor housing to get the desired compressor housing position or just remove the alignment pin. This part would not be too difficult.
My suggestion is to get denco to supply you with a correct casting.
I think it would be quite a severe 'S' shape as that barrel intercooler hangs out quite a bit.
Keep us informed as to denco's responce.
I am in the proccess of fitting an intercooler on my 1hz motor that I fitted a factory turbo from a 1hd-t a while ago. I am going for a air/water intercooler as space is a premium under bonnet of HZJ75.
Looked at the denco setup but found pressure drop too much and poor cooling efficiency.
Denco only manufacture the adaptors on either side of intercooler and brackets for front radiator, the rest (barrel, front radiator etc ) are PWR components. I was not very impressed by denco's responce when I started asking some quite technical questions about their air/water intercooler, they either did'nt know or did'nt want to tell me much.
If you want some serious info on air/water intercoolers have a look at
http://www.are.com.au/ , if you speak to Richard he will give you a rundown about these barrel intercoolers and other options, he is extremely helpfull. I am getting an air/water intercooler core (best available by far) from them and will be manufacturing the rest myself.
Hope this is helps