I've been following this thread with interest, and have a couple suggestions. Some of this is a repeat of what others have already suggested, and I'm just adding another voice in the same direction.
The first one is to leave the breather system the way it is, stock. Running the hose from the timed breather to a catch bottle won't really help relieve crankcase pressure any more than the stock system. The vent from the oil tank to the air cleaner already does that. If you want to use a catch bottle, just run the vent hose from the tank into the bottle, as you appear to have already done.
Regarding the leak, you've identified it as coming from the cylinder to crankcase joint right at the area where the cases have been welded. Can you tell at this point whether it is coming from the actual cylinder to crankcase (base gasket area, if you have a base gasket), or from the joint in the crankcase halves where the repair is?
If it is from the gasket joint, and re-torqueing the base nuts doesn't help, then I don't see any solution except lifting the cylinder and re-sealing it. If it was me, I'd remove the base gasket completely and just use a good joint sealant (My favorite is Hylomar blue). I've not had real good luck with using base gaskets.
If it is from the crankcase joint, I'd suggest you try a wicking sealant like Loctite 290. Info here
http://www.henkelna.com/adhesives/green ... -13227.htm
I've had good luck with it for sealing leaks in joints without disassembly. Be sure and clean the area as much as possible by flooding it with brake/parts cleaner, or acetone, etc., scrubbing with small brush, and letting it dry thoroughly before applying the Loctite. High pressure air and blow gun help. The problem here is that oil in the joint will make it difficult for the Loctite to wick in properly, but it's worth a try. I've also seen a fair number of repairs to crankcases at the track using JB Weld that lasted surprisingly well, so you might want to try that instead, or try both. Again, thorough cleaning is necessary.
That's all I can think of. Good luck with it.
Ken