This is on my 1998 Legacy 2.5 (EJ25D, naturally aspirated, 5MT)
TYPE OF STUTTER/STUMBLE
Steady throttle/Increasing throttle/Both: Both, never at WOT. Only on the highway over 59 mph/~3k rpm and part throttle.
MODS
Intake: none
Exhaust: uel header, tsudo high flow cat
Fuel: none
Engine Management: stock, with a grounding kit and big 3 kit
Has STi Group N engine, dogbone, and transmission mounts
MAINTENANCE
Sensors changed: Upstream O2 with a Denso, and ECT with OEM about 5 years ago, MAF cleaned at the same time. MAP swapped with known good one off my other Legacy that does not have this issue, no change. Knock sensor replaced with OEM about 3 years ago, torqued and angled according to FSM instructions. CKP, CMP, and TPS are all original.
Plugs changed: NGK laser platinums, 42k on them
Coil Packs changed: MSD 8239 coil pack, 33k on it. Wires are NGK blue with about 25k miles.
OTHER SYMPTOMS
Check Engine Light: Rarely ever throws a CEL while stumbling. The couple of times it did, it had misfire codes on all 4 cylinders. Right before it started stumbling it was throwing an EGR Flow code (P0400) at about 50-55 mph in 5th, and weirdly not since despite no parts replaced except all the small diameter rubber vacuum hoses in the engine bay as they were old and hard, which did not make it stop throwing the EGR code.
RESULTS
What has and hasn't worked for you: Noticed header was cracked in front of the upstream O2 possibly causing false air readings, replaced it today along with all associated gaskets. It behaved for the initial test drive, but I drove it again later today and it did it again. Putting 87 octane gas instead of my usual 89 made it slightly less worse but that could be a red herring.