04 Sienna charging problem

A friend of mine was changing the alt.belt and somehow grounded the battery feed cable on the alt. He called me to come check his taillights. He had no break, tail or turn signals. That's when he told me about hitting the alt power cable with a screwdriver. I checked the Alt-s fuse it was good. Then I noticed the main fuseable link was burned in two. I replaced the fuseable link block. I got running lights and break lights but no turn signals. Checked fuse for turn signals and have no power to it. Also after replacing Fuseable link block I checked to see if alt.was charging, only 12.04v and steady dropping as the engine ran. I figured the voltage regulator had shorted out too. So he got a used alt.and I put it on and got 11.59v from it I rechecked the fuseable link and alt-s fuse both are still good. Figured he got a bad alt. from the salvage yard so he got a new alt from parts store. 12.14v and dropping as engine ran. Changed battery with a known good one and got 12.14v but when it dropped to 12.11v it held. Even with my charger hooked up only reads 12.14v until the ignition switch is turned off then it shows 13.59v from my charger. I'm starting to think there's maybe a bad ground somewhere. Does anyone have a suggestion on what else to check???