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Discussion Starter #1
Just some background:

-2006 Murano S
-141,xxx miles
- Battery less than a year old

I encountered the issues in this order:
1. - Battery wouldn't charge - got alternator replaced
2. - Next day I was driving(at this point in time my exhaust manifold was cracked so the engine was running a bit rough) and then the car started shuddering when accelerating. Got towed home, assumed manifold had kicked it completely.
3. - Sat for a bit in my driveway then got it towed and repaired(whole new exhaust system)
4. - When leaving I was experiencing misfires(which i assume was the cause of the horrible shuddering previously in conjunction with the cracked manifold)
5. - Ran codes: p0301 - cylinder 1 misfire. p0603 - Internal Control Module Keep Alive Memory (KAM) Error
6. replaced spark plugs(needed anyway) and switched my cylinder 1 and 2 ignition coils(to test if the coil was the issue and make it easily accessible if so)
7. ran a bit smoother but still misfires
8. Ran codes: C1109 - Battery voltage abnormal. p0725 - engine speed circuit malfunction.

At this point, I'm kind of confused since this issue seems like somewhat of a moving target. I don't want to go ahead replacing things indiscriminately. Was hoping someone would have some insight into this progression of events.
 

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With all the computer controlled systems in cars these days, they require a very healthy electrical system. Weird stuff starts happening when everything is not up to snuff...

Even though you battery is only a year old, I'd have it load tested to be sure it's good. Also have the new alternator checked to be sure it's not defective. Make sure your battery terminals and all grounds are clean and totally free of corrosion.
 

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It seems all the current problems happened right after the alternator change so I would start there. In addition to what MuranoSL2003 suggested, check the condition of the drive belt as well as the belt tension. I believe the 1st generation Murano uses a manually-tensioned belt and it's possible that the mechanic that changed the alternator may not have adequately tightened it when putting everything back together.
 

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Discussion Starter #5
Sorry for the late reply, the wife was I'll for several days leaving me on baby duty.

Battery and alternator checked out good.

I'll give the belt tension a look.

I guess I'm wondering which code I should focus on first. The "abnormal voltage" or "engine speed input malfunction"? On the one hand the voltage thing could cause plenty of issues but with everything testing fine I'm not sure where to go. From what I've read about the other code it indicates a defective engine speed input sensor or transmission output speed sensor which seems more inline with the symptoms, but I could be completely off base about that.
 

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Sorry for the late reply, the wife was I'll for several days leaving me on baby duty.

Battery and alternator checked out good.

I'll give the belt tension a look.

I guess I'm wondering which code I should focus on first. The "abnormal voltage" or "engine speed input malfunction"? On the one hand the voltage thing could cause plenty of issues but with everything testing fine I'm not sure where to go. From what I've read about the other code it indicates a defective engine speed input sensor or transmission output speed sensor which seems more inline with the symptoms, but I could be completely off base about that.
Not sure what to make of those codes. I'd be inclined to record the freeze frame data, clear them and then see if they come back. You said the car "misfires"--have you tried using a scan tool to check the misfire counters for each cylinder? If the misfire is bad enough it should be throwing codes. It could be that the misfire is a separate problem from those codes altogether.
 
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