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14/2 NM cable is not made to be installed in conduit. Your feeder that consists of 2 hots, a neutral and a ground is actually 2 current carrying conductors as the neutral only carries the imbalance of the 120/240 volt feeder. Your 2 conductors for the charger would count as 2 more for a total of 4 conductors. The amperage of the charger circuit is almost nothing as it is a trickle charger. A 20 Kw generator does not product 100 amps. It is actually 80 amps and #3 THHN in conduit is allowed for 110 amps in a residential installation. You are fine with the #3 for the hot conductors. This comes from the 2011 NEC and has not changed in years. Voltage drop is not an issue for 110' of feeder.
The 14/2 is not NM, but UF, outdoor rated. I'm pretty sure that the inspector is going to want the 14ga wire in conduit for the exterior portion, does that mean that I need to go to 14g THHN wire? I'm only going to have 1 entrance for all of the power, (Kohler spec) and 1 for the LV. If I cant run the 14/2 in the conduit with the #3, what would the inspector want to see? Branch it out and re-join?
I can't speak for other inspectors, some have "preferences" they like to require while not supported by the code. UF is treated the same as NM cable. UF is approved for direct burial. This is simply the circuit for the battery charger and is a very low load. THHN would be the correct wire to run in the conduit. Does the generator call for #3 Copper wire? Is it a specification?
Is your transfer switch rated for use as service equipment? Is it the SA7 kit or the SA2 kit?
It is the SA7 kit, so yes it is rated as a service entrance. It does not call for #3 but it has a 100A breaker...
Does this connect to LP or Natural Gas? This makes a difference in the amperage output and the generator rating, 20 Kw or 17 Kw. LP is 20 Kw.
Its LP. So the nameplate has 75A, the 20KW for LP is 83.3A, and the breaker is 100A. I am using THHN-2 for both the #3 and the #14. I've pulled the 14/2 and will run 3 individual runs for the #14 (HOT,RTN &GRD). If I am correct, the 90deg column (applicable for THHN-2) rates the #3 for 110A and the #14 for 25. If I need to de-rate 20%, that pulls the #14 down to 20A, which should be fine, but the #3 down to 88A. Does that meet code?
This is residential. There is a table that says #4 is good for 100 amps residential and #3 is good for 110 amps. 4 - 6 current carrying conductors is derated to 80% so that is 88 amps for #3 and your capacity is 83 amps so no problem at all.
It should not be necessary to run a 2nd ground in the conduit, only a single #6 would be required.