A few months ago I got a 2001 DRZ250 for free, it was tore down because the guy I got it from was going to put the engine into a street legal frame but never finished it.  It was raining last weekend so I started putting it back together, got to a point where I could try to start it but it was a no-go.  Absolutely no spark.

I've troubleshot it down to a suspected bad CDI, but there are none available for sale except from Suzuki for big money.  The DRZ400 CDI looks exactly the same and they are all over Ebay for decent prices.  Has anyone ever tried this?

Looking at Suzuki parts fiche, part no. for 2001-2005 DRZ-250 CDI is 32900-13EA0, and for DRZ400E CDI part no. is 32900-29F60 or 29F10.
On some Japanese bikes, the first set of nos. is the part no. and the rest indicates model and year. I would check with a Suzuki dealer first.
The 250 CDI has a higher price than the 400 by + $100.00

No personal experience of this but, I think if you search these very forums you'll see people have done the swap in the past and report no problems. I THINK, NOT GARANTEED.

I've got a buddy with a DRZ400E, he's going to loan me his CDI so I'll either confirm or deny this.

DRZ400E CDI will work on a DRZ250.  I don't know if it will run exactly the same, but it does work to start and run the bike.

I also found out that if you are using a battery charger to try to start your DRZ250, it won't produce a spark if you have it set at 200amp start mode.  Turns out that my CDI was just fine once I put the charger on 40amp quick charge mode.  I'm glad I didn't buy a CDI.