Mudbath
Old Smoky
These 6.5's can sound like a rod bearing gone when to far advanced. I would try to get it timed, after putting the Heath computer in it could amplify the problem as it does "learn" as you drive it. There still might be a bit of air in one of the lines causing an injector to not work and would be noisier. Start with the timing and then a good run. The fact it did run earlier with out the knock it may not be mechanical. With the valve cover off do all valves open and close when cranking it? You could check that on both sides.