Hi and Welcome
Othere will /may chime in.
1. That is the stock feed for the turbo
2.No keep the mechanical pump you are way better off,is the tranny an automatic or manual?
3 The Previous owner may have made a mechanical waste gate for the turbo,a couple of reasons for that.One is it's been converted to a mechanical pump,and the vacuum pump may have been deleted.If so you may come across a couple vacuum related issues depending on the tranny.
4. I would contact Kennedy Diesel and get a fuel pump wiring harness from him and install it.
5. Sorry i don't have a truck like that running so i can't provide any pic's,they are all under 4 ft of snow.
6.Clean the cooling stack and make sure your cooling system is clean and working correctly,check thermostat,water pump,fan clutch and clean between the rad and AC condenser.The bottom of the fuel filter has been known to rot out.
You should take some pictures of the mechanical pump,the wastegate from the turbo and the leaky fittings for the turbo and post them.Then some eyes can access the work done.
Enjoy the new truck
90 Chev 3500 c/c 4x4,6.2na,400 auto,4:10 gears.DSG Timing gears,main girdle, isspro tach, pyro,boost,oil and trany temp.Dual Tstats, High volume peninsular pump,on shelf, Custom turbo and intercooler 85%complete. Change of plans for the dually, it's going to get a Cummins. Both trucks are Blue 90 4x4 crews