I had to get my manifold milled .250 down to clear the heater box. Also you can remove the plastic vacuum box on the out side of the A/C box . Another option is to find a non A/C heater box , those look like they have a lot more clearance. here is a pic to show my clearance.

 

I'd say you shouldn't have removed the majority of the weld. If you prep the material and bevel the edges to give the weld some place to go you can grind it smooth.

 

Do you have a build thread? Your work is amazing

 

very clean looking ill look into those options thank you

 

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I have not addressed the turbo issue yet have some adapters coming in the mail. I did get the radiator and intercooler installed though I will say using the Cummins radiator has its issues. I thought the radiator Outlet being on the same side as the motor Inlet would be better than having a long cross hose at the bottom but it caused its own issues being so close together would definitely have done it differently knowing that. I will post more pictures later today.