EX60-2 alternator issues

Hi All, i have been trying to fix the EX60 again to day, still not good. i written all details down and will attempt to relay them accurately. many thanks for all the help so far. right here goes.................... 1) 3 months ago battery light started coming on and machine would go into a 'limp/emergency mode' after about 30-40 mins of operating and battery light on. 2) decided to renew both batteries and clean terminals/connectors etc, and have alterntor output checked. 3) alternator output was a bit down and intermittent so fitted new batteries all ok apart from continued symptoms as above. 4)replaced alternator with a NEW 24v 25 amp pattern type NOT genuine Hitachi, battery warning light on immediately and would not go out at all regardless of revs on engine, worse the intake manifold heater is permanently on!!!!!!! machine now stops as soon as key turned to off, which it has never done before. machine operates through all mods ILEP etc fine, tracking speed selection all fine, however the 'auto idle' does not work, revs do not pick up when hydraulics operated. 5) decide to remove alternator and have tested in case faulty, during removal shorted alt against chassis blowing fusible link, should have double checked my mate had disconnected batteries!!!. 6) alterntor tested and all is well, refit, replace fusible link, connect up and start engine! no charging voltage and battery light on constantly, worse the quick heat system constantly heating although light in cab gone out . QHS constantly on, only way to stop is disconnect at solenoid. 7) much checking of contacts, fuses, wires, key switch and general following of circuit and wires. no visible problems, started machine no improvement exactly as above! QHS still disconnected at solenoid, machine stops as soon as key switched off . auto idle still not working (happy to live without it, as i rarely use it). no charging voltage at alternator terminal or batteries. 8) after seeking advice i connect a separate warning lamp in the circuit between battery positve terminal on alt and charging lamp harness connection. start engine and hey presto lamp illuminates, then extinguises as it should and better still charging voltage of 27.8 - 28 volts. also warning light in cab on instrument panel is out!!! however the machine now has to be stopped with the manual pull stop under the seat as original when purchased. 9) decided to connect up without my lamp and try again no charge voltage and machine stops as soon as key turned to off . 10) repeat no.8 above, charging voltage where it should be and all warning light go out, machine has to be stopped with manual stop again 11) i notice a number of 'blind'plugs which i believe are diodes to the right of the seat in the cab under fuse box cover etc they have A1 on one of them and A4 on the other, could one of these be faulty, if so where can i buy them. also one has been looped together with a piece of wire!!! it has a Red and White wire in one side and a red and black i think in the other side, should this have a diode in it? if so what value?? i am really confused by all these symptoms and although i could run the excavator with my additional lamp in the circuit i would prefer to have the machine right and am concerned any bodge to get it working could have a worse effect long term! As always i am in your hands knowledgeable people:notworthy, please any suggestions gratefully received, one thought i have had is whether the pattern alternator is missing some clever part of circuitry that OEM part has inside?? any suggestions PLEASE