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Some info here from our 350 kitted bikes. 350 kit info
I ended up modifying a 450 barrel but you need to make sure you machine the oilways and locator lug sockets to match the 250 barrel. I probably have the details here somewhere if you go that way, if I recall it's some off the top and some off the bottom of the barrel not just one end.
The 350 kit is worth the hassle as it makes for a lighter feeling bike than the 400/450/525 with closer gearing although that closer gearing does restrict your road speed a lot.

 

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I'm fairly sure the water jacket in the 250 barrel is smaller than the 350 piston so you'll definitely go in to it.
This is the detail of my modified 250 barrel, the 450 barrel has smaller water jacket.
"89.4 dia x 99mm liner in what appears to be a 250 barrel with large water ways.
Custom JE piston no 522417 flat top"

Both times we've had steel liners in the 350 kits the bikes suffered from overheating when the going got hard/slow, whereas the nicasil lines ones didn't. I do wonder if you need a slightly bigger bore/clearance to use the 450 piston in a steel bore.

I paid £90 to have a 450 barrel modified plus re-nicasil cost. Second hand 450 barrels are cheap enough.

 

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Pictures are a standard 250 barrel and a modified 450 barrel, I had the machine shop copy a genuine KTM 350 kit barrel but I guess you could get then to copy the 250 dimensions. YOU DO NEED TO GET THE DOWEL LOCATORS MACHINED TO DEPTH AS WELL.
I'll ask the person who did my machining if they will consider doing more but it was a bit of a favour.

 

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PS I'm in south Devon as is the machinist.

 

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I think a 400 barrel would be ok as it's 85mm ish high so plenty to play with.

 

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Stolen from one of KevinYorks past posts.
Deck heights
"450SX/SMR are 69mm
540SXS and 560SMR are 76mm
250 EXC is 78mm
400/450/520/525 EXC 400/520/525SX and 525 SMR are all 84mm"
That would suggest the 400 is the same barrel as a 450 but it's a different part number.

 

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This has been bugging me today so I looked up the 450 barrel on a KTM fiche and it's actually the same part number as the 400 59530005000. If you google the part number it only comes up as a 400 I guess this is because the 400 predates the 450 in EXC guise by a couple of years.

 

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He definitely took some off the top and and bottom to match the genuine 350 barrel I have.
The picture below confirms this and gives you a good idea of the spigot length, you can also see the machining line at about 4mm. You can also see roughly how much has come off the top, I don't think it's critical other than making sure the crank/conrod misses the spigot and the total height is correct.
Looking at the machining marks I'd say it was all milled but it has since been etched by the nicosil process so hard to tell. I'll see if I can't find my calipers and give you more accurate dimensions.
You do need to make sure the dowels are machined to match the cases and head.

 

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Slightly more accurate measurements but battery had failed, I'm sure nothing is taken off the spigot so I make that 3mm off each end to make a height of 76mm and put the chain tensioner in the correct place.

 

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Seems reasonable, mine measures 69mm

 

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And then a kit turns up.
350 kit

 

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Yes, I think you're right, I'd not looked at the pictures.