Scag Turf Tiger Negative Amps And Popping Through Exhaust

I have a 2012 Scag Turf Tiger 61" with a Briggs & Stratton Vanguard V-Twin 35VAC (Model: 610000), experiencing two (2) problems, and not sure if they're connected.
 
PROBLEM #1 - NEGATIVE AMPS WHEN CLUTCH ENGAGED
 
Here are my two (2) scenarios:

1. No Load (Clutch Disengaged) @ Full Throttle:
   28 VAC at Voltage Regulator
   14.4 VDC at Battery
   Positive AMPS on Console Ammeter
2. Under Load (Clutch Engaged) @ Full Throttle
   28 VAC at Voltage Regulator Input
   12.3 VDC at Battery
   Negative AMPS on Console Ammeter

As you can see from Scenario #2 above, the battery is NOT getting charged when the clutch is engaged.
 
So far I have done the following:

1. New Battery
2. New Clutch (properly gapped)
3. New Voltage Regulator (which I moved to the frame to eliminate excessive engine heat to the unit)

PROBLEM #2 - POPPING SOUND FROM EXHAUST WHEN LESS THAN FULL THROTTLE AND WITHOUT CLUTCH ENGAGED
 
Once the engine heats up you can hear a popping sound coming from the exhaust, with anything less than full throttle, and the clutch disengaged. My local dealer told me the usual suspects creating this are either (a) faulty fuel pump or clogged filter, (b) valves improperly gapped, dirty carburetor or, (c) bad voltage output from the alternator to the coils.
 
So, I have done the following:

1. Converted the fuel pump to a low volume, inline, electric fuel pump (GPH and PSI per Briggs & Stratton Tech Department
2. Replaced the fuel filter
3. Adjusted the valve gap clearance

Based on what I have done so far, it looks like I've narrowed it down to two (2) resolutions. First, the carburetor needs to be rebuilt. And second, the alternator needs to be replaced. (I'm leaning more towards replacing the alternator, as it may also be what's causing PROBLEM #1 above.)
 
But before I get into doing either one of these repairs, I decided to post on here, to see if anyone else has had either problem, and what they did to fix it.
 
Thank you in advance for all your help.

As for the PTO causing negative amps it is very possible that you have a partially shorted PTO electric coil. I personally seen in my shop PTO pulling up to 20 amps and still be operating normally as far the engagement of the deck. Normally this electric PTO clutches pulls no more than 7.5 amps max.
 
A short PTO clutch can easily out pace the engine's stator output current. Most Briggs engines have a 15 max stator but there are a few that can produce 20 amps max.
 
By the way the dealer is wrong about the coils are they are CDI magneto versions and are driven by magnetism of the flywheel. If had voltage going to coils it would fry them in short order.
 
Now dirty and worn carburetor components can be cause running problems. Also an overload stator can be acting as an engine brake. Some Kohler engines actually use the stator as engine brake on shut downs.
 
I suggest you reslove the electrical issue first then move to running problem.