ok, at the computer. Your current setup (before the new alternator) was to have the output of the old alternator, via a regulator, go through the ammeter, as Terry mentioned. As you have an ammeter in circuit you can't just ignore it. All the feed for the instrument cluster and the keyswitch, which then means ignition and starting, feeds off that meter. The other side of the meter is then fed back to the engine harness and to the battery, to charge it....
You have a couple of options. For all options, remove and discard the red wire from the old regulator to the starter solenoid.
As the output of the original alternator setup was only 39A and the new one, I suspect, will be at least 60A you can't just hook straight up to the existing wires.
Option 1. If you want to keep everything as 'normal' as it is, and the 2 orange wires are big enough (8mm minimum). You will need to upgrade the circuit breaker to the output current of the new alternator, or it will trip whenever the alternator output goes above 40A. Move the orange wire that was on the old reg to the output of the new alternator.
If the orange wires aren't big enough, you need to run a new pair of wires, one red, one red/white, using 6 or 8mm wire. At the ammeter end, remove and tape back the orange wires. Connect the red/white to the terminal the red ignition keyswitch is on and the large new red to the other...At the engine end, connect the new red/white to the output of the new alternator and the new red to a new circuit breaker (the side that goes to the instrument panel, not the side that goes to the starter solenoid). Basically, just putting 2 new wires in place of the orange wires that aren't big enough.
The 2 yellow wires from the old stator can be either cut back as close to the stator as you can get or just sealed up and tied back. This gives you the existing system with the new alternator and the upgraded wires.
Option 2. Leave the ammeter in the panel and just have it not reading. Add big red wire (6mm or bigger) from new alternator output to the starter solenoid (where the old red was). Tape back the red/white that was on the old reg. At the instrument panel, on the back of the ammeter, remove and tape back the orange that was on the same terminal as the red for the ignition keyswitch, move the other orange wire on the back of the ammeter to the same terminal as the red that goes to the keyswitch (the one you left on there)... This will also not require upgrading the circuit breaker.
Option 3. (my preferred option

) Same as option 2, but remove the ammeter and put a voltmeter in its place.To do that, just do all of option 2, then pull the ammeter out and put a voltmeter in it's place. The terminals of the voltmeter, '-' to any black, the '+' will have the red and the orange....
Option 4. (my least favourite). Leave the ammeter in the panel and just have it reading current drawn (I suspect this is what most people would do, but I don't like it). Add big red wire (6mm or bigger) from new alternator output and starter solenoid (where the old red was). Tape back the red/white that was on the old reg. At the instrument panel, on the back of the ammeter, remove and tape back the orange that was on the same terminal as the red for the ignition keyswitch... This will also not require upgrading the circuit breaker.
HTH,
Chris..........
(I think I got it all

)