I recently picked up a 1978 DT250E that was in rough shape. I am going through the systems and noticed that it has a CDI magneto with the part number for a 1979 DT250. I read that if the bike was made in the second half of 1978 it would have 1979 parts (fine, can live with that). The previous owner had the harness stripped down to the ignition system. The black wire from the magneto goes to the ignition coil and then to the kill switch on throttle mount. The previous owner told me that the bike used to start in one kick and then just lost spark one day. 
I am fairly new to this type of ignition system and from my research it seems that a CDI (non-points) magneto would require a CDI box, which there is none on this bike. Is this correct? Do I need to wire a CDI box into the ignition system or can will it work in its current setup? Does anyone have the correct resistance values for the black wire coming from the source coil? 

Can you give us more information on how you are determining what ignition system you have or that it's for a 1979?  Points are pretty easy to spot as you can see the points through the windows in the flywheel.

If you have points, first thing to try is simply clean the contacts.

If you actually do have a CDI, no way to get it to run on one wire. 

If you can upload pictures to a site like imgur and link them here it would be very helpful. 

Some background on the bike - frame number is 1M1-103925
The picture of the CDI magneto is here: imgur.com/gallery/mBbLVKW

I also posted a picture of a CDI test I found in an old manual for DT250's/400's. I performed the test from with my multimeter on the ground (black wire) and the brown wire (from charge/source coil, seen near number "3" in posted photo). I was unable to get any resistance from this test. I also tested the ground to lighting coil resistance and got a reading of 1.0 ohm. Unfortunately this manual doesn't have the necessary reading for this coil so I'm in the dark if this is good or not.

I believe the problem is twofold - 1. the source coil is bad and needs to be replaced, 2. I need a CDi box in the ignition circuit. Does this check out from your experience? Thanks for the help!

Your stator looks very dubious, seems like its been underwater? To run, you will need a CDI unit, and an HT coil. Might be a good idea to try and get used parts, if the resistance values dont check out on your stator?

Definitely a CDI stator.  It's not too likely in my opinion that your fairly low 1978 VIN somehow got a 1979 CDI from the factory.  That requires a different wiring harness and different components. 

It's possible someone swapped stators or something...  certainly it didn't just "lose spark" if you don't have a CDI box. 

If you want to try to get that ignition working, you'll need to verify your flywheel is correct for that stator and you'll have to find a CDI box and wire it up. 

Years ago it wasn't too hard to find a complete magneto points system from a 250 at a reasonable price.  Not so common today.  Best bet might be installing a new VAPE CDI system (buy direct for best price) or look into trying a system from HPI.  Best course of action depends on what you intend to do with the bike.

Agreed.  For cdi input side you need red/white for trigger signal. Brown for source coil power and black for ground.

If you only have a black wire running from stator to ignition coil, that would suggest it is the wrong stator and should be a points type.  Does your flywheel have a cam on the boss?

As markT said.  No way was that setup ever running as is.

Side notes:

Manuals are available in Tech Library here.

Also to counter the "Internet lore" about production, pretty much all the 1978 models would normally have been built in 1977. Normally not many 1978 would have been built past February or March 1978 or so? You might still have a decal on the steering head that lists the month and year of production if you're curious. Member DEET here makes reproduction decals and is likely has more knowledge of this topic than anyone in the world... The later 70's bikes are a bit more rare in terms of restorations but he may have a good idea of your production date if you don't have a decal. (If you care, it really doesn't matter)

As far as Yamaha just installing a 1979 CDI on a 1978, as I said, that's not very likely at all. And if they did, Yamaha was always pretty darn good about documenting the VIN when the change took place. I can't find any reference that the USA 250 got the CDI before the 1979 2N6 model. (If it's not a US bike, all bets are off, other countries had different configurations)

Its very likely that a CDI magneto was swapped onto the bike years ago and that the CDI box was lost (previous owner didnt know much about it). The flywheel is stamped with F3T357 (imgur.com/gallery/ocz7kXb) (its in rough shape as well). Is this the correct flywheel for a CDI type magneto? or should I be running a points type? 

Regardless, it seems that I will need a new magneto - the question is whether the flywheel works with a CDI or points type. I see that Rex's speed shop (www.rexs-speedshop.com/) sells full ignition systems. Has anyone had any experience with them? Are they reputable? This is the correct ignition kit for the flywheel I have - www.rexs-speedshop.com/product/dt250-mx-...electronic-ignition/.

Reviews are hit and miss on Rex's. If you don't have any issues, they seem fine.

Most people with issues complain about "lack of service after the sale". If you are not in the UK, getting help or replacement appears to be more difficult from what I've seen.

Your flywheel number does match the Rex listing so it should work with their kit. I don't have one with that number lying around to verify if it has a points cam on the underside or if it's CDI.

I'll read fully later but you should have up around 350 ohms from the source so be sure to have your meter set high enough to read that high. But i'm old school using an analogue meter. I guess ya using digital so i'm lost.
Pulser coil is guessing 100 ohms. But at this stage any reading would be a bonus.
It looks too good to be faulty looking at the image .
So if you have ohms--any ohm--then spin it up with a reverse drill & see what voltage you can get. I use a peak meter so get double but with a std meter say guessing 80 ac volts on the brown & 20 or so on the white/red pulser.
Best not follow my ideas but i have an old 360 running purely using the source & an LT50 Suzy Coil/box combined LT50 RG50 any of those that run a system like that. Just thinking Cheap cost at this stage. Seems odd that there's no cdi box hidden somewhere although it's a year earlier than the stator someone's fitted which has to be "79 unless it a 400 same stator from "78 or when 400's changed the that type stator. Here's an LT50 coil/box. I'm playing on a computer that misbehaving so i'll go check my regular one. Hope it makes sense, & if you decided to experiment my way be sure to strobe it spinning to get a reference but mine was spot on & runs good with flywheel on the crank key & didn't need to change timing as was in the ball park. Welcome too sorry, should have said that first. I'm in NZ so a world away. Now i'll fully read the story--late as usual.
Sorry link didn't work as intended.