Looks like there is either a leaking heater core or failed heater box to firewall seal on the passenger side. Rot repairs can be few hundred to several thousands of dollars, depends if you want a show truck or just want to keep your feet dry.
I should have been more specific. I was refering to Riley's image of a fuse panel, the spot for the second flasher (missing?) is out of the frame. I also noted that there appears to be wrong amperage fuses in some of the spots. Lack of headlights could also be a faulty floor switch.
Should there be two flasher relays? One for the blinkers and the second for emergency flashers. When I had dead headlights on my old '84 it turned out to be a bad fusible link near the starter.
Does the '79 have a floor mounted high/low beam switch or column switch?
The 4l80e should have a factory stand alone controller, maybe behind the glovebox. I have a '93 w/a mechanical injected 6.5td and a 4l80e, I'd check but it's covered with snow.
I believe 6.5TD vans and Hummers have a center mount turbo. A body lift kit is needed to use a passenger mount turbo in a squarebody for the down pipe to clear the heater box and firewall/floorpan area.
If the t-stat craps out with the sender located on the housing, then the engine can overheat. I have never seen a set of headers that block the sender from being located on the head.
Buy an autometer diesel tach part #3788, clamp the pickup to the housing, follow the instructions and you are good to go. KISS, there is no need to re-invent the wheel.