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I just rebuilt the bottom end of a 2004 CRF250R and it is leaking oil from the case gasket. I torqued the bolts to 7 ft-lbs in a criss cross pattern and cleaned the mating surfaces very well. New gasket of course (Vertex). The left case is new and the right case is the original. Any ideas as to why it would be leaking? One thing I found odd is that the service manual says to torque down the transmission drain bolt first, then tighten all of the case bolts. Seems backwards to me. Wouldn't that potentially lead to the cases not seating uniformly?

The only thing I can think of is like a head when it gets hot can warp causing a leak. So maybe the old 2 case halfs were mated perfectly and may have just slightly warped together and the new case half is true causing a leak at the point where the warp is not creating a perfect seal?

I assume you did not scratch the surface either, as that could cause a leak.

That's what I was thinking too. So what is the solution? Get the engine up to operating temperature then loosen and re-tighten the case bolts? Maybe double up the gasket?

The re-torquing idea is worth a shot.
Do not put two gaskets - that just gives more area to be prone to failure under crank case pressure. If it worked it would probably be short lived.

End result for correcting this unfortunately may be split the cases and inspect. The failure area may need to be surfaced to true up to the other case. Also applying Hylamar sealant to the surfaces with the gasket would probably fill the area that is causing the problem. I have seen it have incredible results fixing leaks in aerospace turbine engines that are subject to extreme temps and pressures.

Try the re-torque - cross your fingers - but don't hold your breath.

I noticed in the 2004 250R manual that it says to torque the transmission bolt first, then torque the crank case bolts. This seemed counter-intuitive to me, but I did it anyhow. I'm wondering if this could be contributing to the problem, or perhaps the main cause. My 2007 250X manual says the opposite--tighten case bolts then transmission bolt.

Is it possible to force this stuff in between the case halves without disassembling the entire engine? For instance, could I loosen the head bolts and raise the head up high enough to clear the dowel pins then potentially separate the cases enough to force some Hylomar in between using a toothpick?

You could try. I would probably take it apart and go get case sealing silicone like they use on older bikes pre gaskets. Then join them with that as it will form to the changes. Or use something the RTV black which is the high temp oil resistant silicone. Put a light layer over the entire gasket. I did this to a clutch case side cover that someone scored and was leaking to seal it up.

Otherwise you can try re torquing the specific way the manual says and make you spiral out from the center to try and work the warp out.

Can you see any deformation where the actual leak is ?? (anything look odd ?) , does it look like the gasket is in place and not mushed out anywhere ?? (or in too far*most likely where the leak is*) , if the gasket got pinched and is thin in a spot it may be the issue , if oil got into the gasket material , you might have a issue keeping it sealed at that spot even with sealer

Hopefully the re-torque works [-o<

If re-torque does not fix it then it's time to disassemble and inspect. That's the right way to do it. Inspect, assess and correct.

I failed to mention that the left case is brand new and the right case is the original 12 year old case. Perhaps the left case is perfectly true whereas the right case has slightly warped over time and that is why there is a leak. I'm hoping re-torquing will do the trick because I'm not looking forward to tearing the engine apart a couple months after having put it all back together. The bike runs great by the way.

if oil got into the gasket material , you might have a issue keeping it sealed at that spot even with sealer

What do you mean by "gasket material"? The gasket itself is now saturated because of the leak. Are you saying I'll need a new/dry gasket?

It is possible , if the gasket material was compromised enough and is saturated enough it might allow the oil to continue to pass thru it and the sealer/silicone or whatever may not adhere to the gasket , allowing the oil to continue to flow thru where the leak is ...follow ?? , in other words if the cases are tight , and the gasket is leaking , then there is most likely a compromise or gasket damage or deformation allowing the leak, not saying its the case , just saying , if you try to seal it and still notice any seepage or it actually leaking afterwards , then yea , you will have to start over and replace that gasket..... , hoping it does not happen , but keep a eye on it , you will know pretty quick especially after a few heat cycles