I do have quite a bit of experiance with the 540 but mostly in stock form so I'm no expert on getting the most out of these engines with mods. The guy that bored cylinders and fit the pistons is (Pete Nydall, Nydall Crank and machine). Pete worked for Olaf Aaen for many years and has owned his own shop for quite a few more. He still does alot of work for Olaf and is only about 10 miles form him. Pete is now big time into boat racing and has won national points chamionships in some classes. Pete looked these cylinders over and said they were done right by someone that knew what he was doing. He asked if the head was cut and after measuring the intake ports said it should be cut a .010. I brought the head with when I picked up the cylinders so he could check it out as well. It was cut .010 and Pete this setup should run real strong. He suggested 3 degrees of timing advance and Aaen pipes. He also said that the bored 38's were all that was needed but to gut the airbox and rejet with the powerjet dissabled. He figured it should be running at around 9000 rpm for peak performance. He also said Aaen pipes are a 10hp increase over stock on a stock motor.
Dynotech did a pipe test on these engines both stock and with the updated porting specs that came out. They tested stock, cut stock, Aaen and PSI pipes. They made the most HP with stock pipes but did say that with more mods and higher RPM's the others would probably do better. I think it was Tim Bender that did the cut pipes when he was oval racing these sleds. Delaughter also builds engines and makes pipes for these and I guess his engines are very stought but I have no experiance with them.
As far as me recomending pipes for this set up I would have to say it will depend on what you want to do. If you want to be able to run stock 600 class run the stock pipes or stock cut pipes. If you want to go improved or mod go with Aaen, PSI or Delaughter. I am not sure what they cut on stock pipes to modify them but I will try to find out. There is not alot of free info out there on these engines so it's kind of hard to find. Olaf Aaen, Tim Bender and Delaughter are the big names I hear of that know the most about them.
It will take some testing to get this setup dialed to perfection but what's here should be close. Hopfully there are others here that know these better and will chime in with more info.
Thanks for your interest, Phil (opsled)