94 XR600R engine noise, no idle and backfires

I have an XR600 frankenstein bike that we built for my brother using parts from a 93 XR650l and a 94 XR600. It is basically a 93 650l frame and suspension with a 600 motor and plastic. The motor was cased on a rock on the right side by the guy we got the parts from so the right engine cover was replaced with one off an 89. He is an experienced rider and mechanically inclined , so I have no reason to believe he did not immediately shut it down. When we fired it up the first time it made a knocking sound and did not idle well. Since then I have been through the motor a couple of times and now it has a rebuilt crank with a new IMS hotrod, a new piston (stock compression) and bore (.020 over) and some new bearings and gears in the bottom end. I have not really done anything to the top end other than remove the auto decompression unit that I thought might be a culprit (and was wrong)and replace the cam bearings . After all this, it still has the problem. It pulled very strong when I rode it but the noise was there constanly. It does not seem to matter whether the engine is under a load or not. I can't pinpoint the location because it seems to be coming from everywhere I check. It has sat for a couple of years and I am now semi motivated to either fix it or sell it. I fired it up recently and it has the same symptoms as well as some popping (backfires I guess). I dont rememeber it backfiring before but I could be wrong. I had it on Ebay (it did not make my reserve) and a guy emailed me saying it might be the CDI unit. I have been suspecting something that could affect the timing like the timimg chain, tensioner, or the pulser coil. The CDI never crossed my mind because of the engine noise. Maybe messed up timing could be causing the knock. The pulser coil (by the oil pump)looks like it might have suffered some minor damage in the casing incident from metal pieces being passed around it until the motor was shut off. It seems to be lined up okay. The gap looked a little larger than the service specs, but it still runs so I don't know if that's an issue. Any ideas? Thanks.

Have you replaced the cam chain tensioner? The cam chain tensioners are known to wear out on these bikes but I think it makes a clicking sound. Could it be worn and your cam chain has skipped??

Usually popping and/or backfiring is caused by a lean condition. Could your jetting be off?? If it doesn't idle well could your pilot be plugged?? Leak in the air intake boot??

Don't have a clue about troubleshooting the CDI :)

I have never come across a cdi that could be tested. Usually you have to isolate it. Try testing the other electrical. Pulser coil, coil etc. Hope this helps.

Have considered the timing chain tensioner as a possibility. I also am thinking that there might be multiple problems. Maybe the carb is gummed up after sitting and that explains the popping. My jetting is definately not lean. Thanks.

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