I have just Upgraded my stock 65amp Alt for A 130... here's how I did it.

The stock 87-93 Mustang alt is a Motorcraft "G2" unit
with 5 speed cars having 65 amps and autos with 75amps.
The 94 and up Mustangs and most Fords use the Motorcraft "G3", some 130amp others 90amp.
You can choose to put the 90amp units as well. Anything is better that the "I have my lights on I can't run the a/c" 65 amper.

What I bought...
Bought the upgrade 4 Gauge power wire from Pa-Performace.com $49 (comes with 120amp fuse & holder)
Bought the G3 conversion kit (the plugs for new alt) from Pa-Performace.com about $8
Bought the 130 Amp Alt from Autozone $109. I asked for a 94 Mustang V6.
Bought a 1 1/2 inch bolt & nut..this alt did not have the threads in it for the upper bolt.

How...

Remove the upper Radiator Hose.
Removed Air Filter box & tubing to the throttle body
Removed the Old Alt and wires...then just follow the instructions from the Pa-preformance kit
Cut the 3 wires from the harness the other (smaller) connector plugs directly into the new G3 alt.
Place, crimp & solder eyelets to the 2 10 gauge black & orange wires
crimp & solder the new harness to the white wire.

I had to cut the alt bracket with a grinder...this took about 20 seconds! Test fit the new alt to make sure it now clears the bracket. Some mustangs have different brackets & you may not have to grind them....always test fit first. Photo shown is after I've removed part of the bracket.

For some reason the bottom bolt wouldn't fit on the New Alt..Grrrrr... wasn't to bad I had to drill out only the lip of the hole...seems like the casting was poor or bad remanufactirung...I only had to drill or lightly grind away to make it a circle so it would fit.

This is where the other side of the 4guage wire connects to. Its the Starter stolinoid, inder the plastic cover near the washer fluid reservoir. Unbolt the positive bolt that the positive cable is attached to then put the new wire on the same bolt & tighten,

This is what the wires/connectors are too look like. - The 2 (10 gauge) Black/Orange wires now each have an eyelet - The White wire has the small connector - The Original small oval plug stays the same Not shown - large 4 gauge power wire that bolts to the same stud on the alternator with the 2 new black/orange wires.

That's it... plugged all in with the new 4 gauge wire to the stud on the alt with the 2 10 gauge wires.

The 4 gauge was routed behind the radiator under the radiator brackets and to the + side of the starter stolinoid.

ALT UPGRADE LINKS :

Be Aware that all Replacement / Remanufactured Alternators are not clocked correctly.

I've recently noticed this when I needed a quick replacement alt for and 87 5.0/manual trans/A/C. I will assume its true for all 87-93 V8 Mustangs. I looked at these alts from AidAuto, Autozone, Pepboys, Straus & Ford & were all the same.

On my 87 (5-speed) The different clocking was too far off to plug in the plugs.
You will need to re-clock this.

Most of the stores will sell the 75Amp (which is better but still low) unit even though the manual stangs(87/93) came with a 65Amp.

The Stock 87-93 alts are called "G2" Units...but you probably don't really need to know that.

On my 87 5.0 the alternator light would flash intermittently, thinking that the original 149,000 mile alt had worked longer than I would expect it to & that it was making its last volts, I was planning to upgrade it to the 130 amp unit (see tech section) and thought it was time.

Because of the intermittent blinking I was concerned that a wire might be loose or had a bad connection. It turns out that all it needed was to clean the connections to the alt.

Slowly pull out the 2 connectors to the alt & clean out the oxidation on both alt & connectors, I also sprayed silicon into them thinking that it would reduce moisture & further oxidation. The result: no blinking alt light.

Again... there may be other reasons for the same situation with your vehicle but this may help those who suffered from my exact problem...