My 2000 dakota has started missing - if i push it hard it will even backfire - it appears to run perfectly smooth in neutral even if i gun it - it only misses or backfires when in gear - this problem just began a couple weeks ago and has been worse the last several days which have been extremely cold for Alabama so I dont know if this is part of the problem or just making it worse - i have already replaced one of the controls (some kind of electrical part a little larger than a spark plug) that kind of sticks into the bottom of the transmission so i am wondering if i have another electrical problem associated with transmission or something like that

For 5 miles it is running on choke. Try cleaning the Throttle Body and MAF.

If that doesn't work, you need an auto electrician with a pro grade scan tool computer. It can record exactly what goes wrong at 5 miles and diagnose the fault.

It appears to be a known fault

https://www.google.com/search?q=1998+Dodge+Dakota%2C+5+miles+then+stalls

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It sounds like your timing skipped

A tune-up is always a good idea. Is the system running rich or lean? Any applicable trouble codes? Is it back firing out the exhaust? If so, I got two thoughts, either an exhaust system problem or exhaust valves?

Check your ECT Engine Coolant Temp sensor as it may be running too rich. The cat or muffler can cause back pressure also.

Backfiring is usually associated with a lean condition. Is fuel pressure correct? Is this vehicle TBI and are both injectors working properly? If timing related it should spark rattle under load and the timing would be way out and not run/start well at idle

It sounds like you need a good tune-up, such as spark plugs and/or wires. They will act up when cold and when warmed by engine temperature will let the engine run smoothly again. And possibly a distributor cap/rotor.

Push rod,you have two different size,or firing order is wrong. The intake push rod are 5 3/4 inch long, the exhaust are 6 inches long,Disable the spark and crank the engine the sound should be smooth and even,if its not correct the push rods.If it is correct the firing order

have you tried removing the idle speed motor and cleaning it with throttle body cleaner, as well as port it is removed from?

Breaking up like you described can be related to a condition where the distributor drive gear is wearing out.
Had you checked it for rotor tip travel (about 5mm of loose travel is the max) or had the distributor indexed? The indexing procedure appears to be similar to an ignition timing adjustment but isn't the same.
Chrysler TSB 18-08-93 Rev A describes a condition often seen on the 1992-1993 3.9 engine. The distributor drive gear wears out prematurely and then wallows out the support bushing in the engine block. Your oil pump is driven by the same gear through the distributor shaft, so cold engine operation often is worse from the higher viscosity of the oil and the resulting load it places on the worn parts.
The distributor index slips to the retarded zone (trails what it should be) just from the gear wear. Adding in the worn bushing and chain stretch can put the distributor in a position where ignition cross-firing can occur and the switch plate (cam sensor) within the distributor can drop out-of-sync with the crank sensor.
If you haven't done so, check this out for me. Remove the distributor cap and twist the rotor clockwise and counter-clockwise. The total tip travel should not exceed 5mm, which is just about 1/8". Even if it exceeds this, an adjustment/ indexing of the distributor will get it running right again if only for a short while.

The first thing you need is to have the unit scanned. Check things like the baro sensor,map sensor,coolant temp. and the TP sensor.Also check your fuel pressure,volume and injector spray pattern. I think you will have found your problem,but if not hit me back with engine size and any codes,Good Luck.