I have a 2000 FXST while riding about 30-35 mph I noticed a swishing sound coming from the bottom end,sounded like the primary chain was making noise.A few miles later sound got louder, almost like crunching sound. I shut the bike off, adjusted the primary chain, it was very loose. I start the bike back up, it starts running rough, then starts popping out the exhaust.

The primary chain is supposed to have 5/8 to 7/8 inch up and down play in the top run of the chain with the engine cold. I think it's 1/2 to 5/8 inch hot but I've never set the tension on a hot primary chain.

But, if you say you heard a crunching noise, then the engine started running rough and popping out the exhaust, I'd suspect something to do with the ignition timing. The ignition timing is controlled by the pulses from the crank position sensor on the right flywheel.

If I were you, I'd pull the primary cover, take the compensator sprocket, primary chain, and clutch assembly off, pull the rotor and the stator of the alternator. Then pull the sprocket shaft seal out and take a look at the Timken bearing. While you've got everything off, take the plugs out and turn the engine over and feel for any roughness. It may be time for an engine overhaul. I've only seen Timken bearings fail in one Shovelhead engine but they do fail. Hopefully, you'll find something much simplier and less expensive than this wrong.

Good luck
Steve