The stock charge wire on the LS1 F body is 6AWG. 6AWG will carry 100amps just fine. That should be plenty.
http://www.powerstream.com/Wire_Size.htm
Yes the alternator is MAX rated for 105-145amps but it rarely will run more than 2/3 of the rated current. The battery and alternator will not last long if you are pulling close to 100% rated output continuously. They aren't designed for that.
The first thing I'd do is break out your good meter and run some static voltage drop tests to isolate which cable is causing the problem.
Check from the battery to the engine block circuit and the battery to the alternator BAT circuit with the ignition on and engine off. If you have larger than .1vdc drop then try to isolate which connection is loose by testing at each connection point running back toward the battery. I bet you'll find a dodgy cable or loose/corroded connection. Fix em and you'll have a more stable charge.
#2 would be to make sure the Sense lead to the alternator regulator connection or the PCM is making good contact at each end and is not damaged or spliced in some dodgy fashion.
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1959 M35A2 LDT465-1D SOLD
1967 Dodge W200 B383, NP420/NP201 SOLD
1969 Dodge Polara 500 B383, A833 SOLD
1972 Ford F250 FE390, NP435/NP205 SOLD
1976 Chevy K20, 6.5L, NV4500/NP208 SOLD
1986 M1008 CUCV SOLD
2000 GMC C2500, TD6.5L, NV4500
2005 Chevy Silverado LS 2500HD 6.0L 4L80E/NP263
2009 Impala SS LS4 V8
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