Definitely the rods

Until the experts show up, here's my take:

I wouldn't expect the chain to cause hesitation when coasting or gently accelerating. As the chain wears and IP timing slips, there'll be a general loss of power. Across the board. There's a centrifugal advance mechanism in the IP timing sprocket. IP timing will advance with engine rpm even with a tired chain.

I don't subscribe to 'coming due' for a timing chain. It's within spec or it isn't. At best you've noted a trend over a series of documented checks showing it's about to cross from being in spec to out of spec. Even MB that has a service interval for brake fluid and fuel cap gaskets has no time or mileage interval for replacing a 603 timing chain.

I would guess the hesitation is more related to the injection subsystem. Maybe you do a lot of short trips, stop and go driving and sitting in traffic. An Italian tuneup should blow out the cobwebs. Consider also a bottle or two of Diesel Purge.

Since you mentioned vacuum lines, maybe the EGR valve is stuck open. Maybe the turbo impeller isn't spinning as freely as it should because of bearing wear or coked oil.

Sixto
87 300D