Inconsistent strange noises from upper engine

Hello 5.0 engine experts. I have a clicking, clattering, ticking noise that I can hear thru my Systemax intake manifold but it does not make noise consistently. Let me start from the beginning to know the whole story on this vehicle I purchased a few months back.

I purchased a 1990 5.0 Mustang LX with EFI and is the roller cam motor. The engine has a Holley Systemax intake and Holley aluminum headswith 2.02 valves, aluminum roller rockers with studs and guide plates. It also has a hydralic roller Lunati cam with a .512 lift and 224 duration. The engine had a clattering noise. Upon checking the rocker arms I found 2-3 that were worn and had to much clearance in the trunion. I installed 1.6 Comp cam stainless steel roller rockers. Started the engine and still had some clicking and had a couple of loose rockers so I thought the lifter were bleeding down and replaced the roller lifters with Ford Motorsports replacements. This motor has the stock Ford spider legged rev bracket with the u shapped lifter holders. I started the engine and still had some clattering and clicking so I torn it down again and rechecked the old aluminum rockers to the new Comp's. I could see that the position off the roller was not correctly positioned on the tip of the valve and opted for new correct length pushrods. Installed them and still had the same sounds. Upon tear down this time i noticed that some of the push rods were out of the lifter cups and after looking closer noticed the top edge of the roller lifter had broken off 15 of the16 lifters. Now very frustrated called Comp cams and spokto a rep whom advised I check to see if the guide plate slot was deep enough. Finnaly determined to deepen the slot and that gave me the correct geometry.
Now I have pieces of the lifter in my engine so I decided to tear it down and rebuild while its apart. Opted for a 331 stroker with all forged steel and Mahle pistons. Had machine shop assemble the short block and recon the aluminum heads. Assembled motor with a new set of FOMOCO roller lifters and the existing cam and rocker arms. Adjusted the valves by turning the lock nut to zero lash and then 1/2 turn more and everything looked fine. Cranked the motor over a few times and all is well on the adjustment. Re-installed the motor and fired it up. Sounded good and then I installed the cat back exhaust. Well guess what the clicking clattering noise is back. Noise occurs every couple of seconds and does not have consistent sound
I and my mechanic friend are baffled. Anyone experience a problem like that. Do I need to invest in some of the rollerlifters with the link that attaches the pair of lifters together and eliminate the factory rev kit? Any help would be appreciated. Frustrated in Phoenix.........