I am in the process of upgrading my 68 charger as per the MAD electric amp gauge bypass diagrams. I am going to install a 100 amp 1 wire alternator and perform the amp gauge bypass as well as run a larger charge wire from the alternator to the starter relay. My question is regarding the use of fusible links or is it better to install actual fuse holders in line? and what amp rating fuse or fusible link should be installed? Dash side wiring will be all stock with no additional draws on the system.

IIRC Mad recommend 5" of 14 gauge fusible link added to the end of a 10 gauge wire, from Alternator to starter relay.
Good info and a chart in this link:

http://www.allpar.com/history/mopar/electrical.html

What Pynzo said, I believe they want 4 numbers (2 sizes) larger (which as you know is smaller gauge) as they only go up or down in even numbers so a 12 GA FL in an 8 GA wire is (2) sizes. I ain't up on electronics but I'd prefer a circuit breaker of the right type. I had a 66 dart that by itself overnight (diode in alt I believe) acted up & the wiring from alt to bulkhead & more/some on bulkhead to batt iirc was severely melted & the FL did not open

With a 100A alternator and output stud to fender relay wire, agree 8 gauge wire and a length of 12 gauge fusible link is good.

With a one wire, voltage drop in the charge wire is not compensated by remote sensing that ups alternator voltage to compensate... so the charge wire needs to handle typical current with minimal drop. If you have added non-stock accessories (eg fan, stereo, fuel pump, fans) that increase current draw, bigger wire is better. If electric load is increased, 6 gauge with 10 gauge fusible link would be better. I run this setup and has been trouble free.

AP stores rarely carry fusible link in 12 gauge or larger but "auto electric" stores generally carry at least 10 gauge.

NAPA also carries "maxi fuses" in high amperage ratings. If you use the fuse in place of fusible link, suggest at least a 125 A fuse with 100 A alternator. And get a spare for the glove box.

Thanks all for the helpful information. Looks like I have some wiring to do.

You are doing yourself a dis-service by going with the one-wire alternator. Be sure the alternator you do use puts out a lot of amperage at idle. Most don't.

I agree with JBC

I am not sure I understand the real need for a fusible link where there was none. It does add a minor amount of resistance, and I thought there are reports of links opening with unpleasant results. There are a lot of cars that don't have this extra "safety" measure. I would think a true battery cutoff switch manual would be less headache and better in any full blown meltdown scenario.

yeah that semi melted insulation on the firewall on my '66 dart was an eye opener for me & left a lasting impression (No mas ever again if I can prevent it). not sure what the solution is but its on my mind

I totally agree. I had bought and was ready to install a Fuse Link into my upgrade engine harness and decided against it. Ma Mopar didn't use it, why bother? You connect the Alternator output directly to the Starter Relay Stud, the Battery Cable hooks up here(unfused), and from here a 16 gauge fuse link feeds power to the dash harness.
Is there really a need to fuse the Alternator also?

I had My 70 Charger fry the harness when the Alternator shorted. The Amp wire melted and shorted to a hot ign wire and the engine would not shut off.Now on My 68 R/R the harness is out for restore and that same ckt is melted. I have a new firewall plug coming and will modify,get rid of the Amp gauge ckt but leave the gauge in. I will use an aftermarket Volt meter.You would think MaMopar would of put a fuse link in there as a safety. Silly engineering if you think about it. Where is Ralph Nader when you need him. HA.

I don't understand the need for a fusible link even when there was one. A piece of wire that goes bad and doesn't always visibly show it= DUMB.

A fuse or breaker would be my choice.