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Welcome to the forum.

It sounds like you got a Frankenstein there for sure. If I sold to it to you, I would make sure you could not get hold of me after the sale too.

I'll try to help you as much as possible - lets start with the VIN off the frame and the serial number off the engine.
 

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Thanks!! And yea tell me about it haha. I appreciate the quick response though! The engine serial number is “T521E-8720699” and the frame says 2004 trx250TM
Both the TE & TM used the same range of engine serial numbers:
2004 was TE21E-8800001 and UP
2003 was TE21E-8700001 and UP
02 was 8600001 UP and 05 was 8900001 UP

I think you have an 04 with an 03 engine

VIN'S were 478TE210444400001 and up - note the 9th character will change with the last 6 digits - the last 6 are the production sequence and the 9th is a check digit that is either aplha or numeric determined by an algorithm - the first 3 identify that it ia a Honda made in SC - the next 5 digits identify it is a TRX250 Recon - the 9th varies - the 10th digit is the year - the 11th digit indicates the plant (4 is Ashville, SC) and the 12th through 16th is the production sequence. Your has been painted over, but 478TE21044 is clearly visible to me, so according to Honda's ID Guide it is an 04 TRX250 Recon - whether it is TE or TM is totally dependent on the engine and wiring.

Now the connectors may be different, but the biggest difference in the wiring is the electric shift motor, the angle sensor and the electric shift buttons.

If you plug in the stator, pulse coil, neutral and reverse switches, it will work as a TM (TM was 2x4 manual shift, TE was 2x4 electric shift) - so all you need to do is get the correct wires connected.

Here's the TM wiring diagram
4788
 

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Well, it is the correct motor, just a different year with some shifting options that you will not be using.

The ignition was the same up to 05, so having an 03 motor in an 04 frame should not be a reason for not having spark. Here's the ignition system isolated from the rest of the wiring:
4789

Here's something you don't know - the ignition is AC (like a lawn mower) and does need the battery to generate spark - the battery connection is only so the neutral light will work.

The ignition control module (ICM) needs a ground connection on the light green wire for starting - the blk/wht wire kills the spark by grounding the ICM, grn/wht is frame ground. So if the light green wire and the green/white wire are grounded and the blk/white wire is not grounded, then you just need specific voltages on the blk/red blu/yel and blk/yel wires to get spark.

You need a peak voltage tester to read the voltage - typically the exciter coil generates about 45 volts peak, the pulse coil about 3 to 5 volts and about 100 volts on the blk/yel wire going to the coil.
 
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