If the alt/reg are good/grounded and you jump fire to them directly and the green wire connecting them has continuity then they MUST charge. We're missing something. We need a diagram of how things are wired now to proceed. The most common prob with batt in the trunk is too small of cables but we have other issues that must be taken care of first. Post a diagram when you can. What I prefer with a batt in the trunk is to run the 2/0 positive cable up to the starter large lug (hot all the time but welding cable ain't gonna short (has very thick insulation) & you dont lay it next to sharp edges when you are routing it front to rear) then run an 8 ga from starter large lug to starter relay large lug & ammeter in series in that line between the two then run a line from the large starter relay lug to the bulkhead/interior to power everything. I run the alt to the starter relay large lug. EDIT "it wont shut off". The ign sw ign1 (run) terminal should be wired to open/close current to the reg/alt/coil/ECU. I should bone up on the Madd conversion but something did get crossed there. Their conversion is sound if you dont mind losing the ammeter function and have accessories that are drawing alot of current from the batt side and you dont want to route all the current to replenish the batt from alt to bulkhead then inside the dash then thru bulkhead again then back to battery. I prefer to bypass the 2 main in/out wires in the bulkhead/relay add ons directly to the source (the alt) that will be powering them and keeping my ammeter (plus adding a voltmeter to switched 12V)