Clunk on acceleration or under load

[Firebob462]

The only thing in a 30 or 40 series TC that can make a clunking noise is the flyweights in the driver/clutch, and I doubt that's your issue, it would have done it before also. Betting the ex's share of the 'farm' you're torqueing the chain loose now that there's a driven with a symmetrical belt. (Wondering how that asymmetrical 30 driver worked with a V-belt, or vice versa, whichever.)
Chain may be tight right now, but under load the mount may be flexing, loosening the chain for that moment, and letting it skip teeth with a clunking noise for sure. Stop to check, chain's tight again. Had the same issue for a couple of reasons at once.
First, I went OCD on vibration and used both hard and softer rubber grommets on both sides over/under the motor mounting base, and they compressed under load, making chain skip. Tossed the top ones, better but not enough. Replaced a couple of softer ones underneath so all 4 were hard rubber, made it correct.
Found then that 17" long too-thin motor mounting plate I only supported with 1/2" angle iron on 1 side was flexing down under load, same result. Added angle on other side, got it close but no cigar. Added a cross-brace at 11" mark, finally solved everything. Get the picture? Stuff you can't see while under load unless you had a GoPro aimed at chain/sprockets. Invisible problem when inspected, ghost in the machine.

Interesting this makes me wonder if I put the wrong bearings in my jack shaft. I put in 5/8 pgn snap ring bearings whiched replaced the standard lawn and garden style bearing. The jackshaft has a round 3 to 4 inch pipe that the 5/8 jack shaft slides into when inserting in the the jackahaft housing. The lawn and garden style bearing have lips on them that the round inner core of the jack shaft could potentially ride on. Being that nothing is supporting the round inner sheef that the jack shaft slides in I'm wondering if this could cause the shaft to flex during load which would loosen up the chain. I may be over thinking it but do you have any experience with the old yerf dog jackshaft set ups.