I have a 1993 dodge dakota with a 3.9L V-6. My question is what do i need to do when the trouble shoot code 41 shows up which means the generator field isn't switching properly?

You're not going to get a satisfactory answer to your problem. In 1996, Dodge (and most manufacturers) went to the ODBII standard to be in compliance with Federal emissions standards. That means that the 1998 engine will have to be an engine only in your 1993 Dakota. No multiport fuel injection with a PCM to regulate injector pulse, ignition, timing, etc. Or anything else that is controlled by the PCM (air conditioning, etc).
Your options are to connect what works from your 1993 engine wiring harness, and replace any items that have no connection. Or you can try to adapt your 1993 truck to the 1998 engine harness, and use all the goodies that came on the 1998 engine. But you are going to need the expertise of someone VERY familiar with both generations of Dakotas. Good luck.

To read these you break them down into 2 digit numbers:
12 Direct battery input to PCM was disconnected
41 Generator field not switching properly
11.Timing belt skipped 1 tooth or more from initial learned value, Intermittent loss of either camshaft or crankshaft position sensor, No crank reference detected during cranking.
55. END OF CODES.

12 is normal and 55 is the end of the sequence

The 12 is normal for the starting code. The 41 says generator (alternator) field is not switching properly. Code 45 says Turbo boost limit exceeded (engine was shut down by logic module). I doubt that you have turbo on the Dakota. However there IS a code 46. Battery voltage too high during charging or charging system voltage too low. That would make sense with the 41 code. Sounds like you may have an alternator/charging system problem.

On a dodge all you have to do is turn the key off and back on again 3 times. The codes will show on your dash.,

Chrysler Fault Code 41: Alternator field control circuit open or shorted
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WHEN EVER YOU WATER IN THE OIL IT'S NOT GOOD TWO POSSIBLE REASONS BAD HEAD GASKET OR BAD CYLINDER HEADS

I will look in my 1992 service manual & post later today.

Hi There.. firing order for 1993 Dodge Dakota 1-6-5-4-3-2

the trouble codes are as follows code 12 problem with battery connection. direct battery input tp pcm disconnected within the last 50 ignition key-on cycles. code 15 a problem with the vehicle distance/speed signal. no distance/speed sensor signal detected during road load conditions. code 55 completion of fault code display on check engine light. this is an end of message code. the speed sensor is located on the transmission/transfer case extension housing. check plug connection to speed sensor for power using an volt meter. connect the positive side of volt meter to the orange wire terminal and the negative side of volt meter to the black/light blue terminal. the voltage should be approximately 8.0 volts and to check the voltage from the pcm connect the positive end of volt meter to the white/orange wire terminal and the negative side ti the black/light blue wire terminal. signal voltage should be 5.0 volts. if there is no signal voltage signal, have the pcm checked out. if you have both signals from the terminals then remove the vehicle speed sensor and check the speedometer pinion for worn or missing teeth.

Code 14 is a faulty MAP sensor , and 41 is alternator field control circuit open or shorted. I'd start with checking and cleaning the connector at MAP sensor, and check all connection at alternator as well as battery. You'll need to replace MAP sensor and have alternator tested if cleaning doesn't cure it.