1998 Sienna sputtering/ halting acceleration

We've had a 1998 Sienna for a while now, and have gotten much use out of the van. It has 215,000 miles on it so far.The past few months, though, a couple problems have come up. The first, scary problem was an issue with the timing belt hitting something inside its cover( I was not there to get the full details from the mechanic), causing a clicking sound much like a more serious problem. However this was fixed.

At the same time, the van has developed a stutter (most noticeable in lower RPM's, but you can sometimes feel it above 1700) that really shows up during slow acceleration between 1400-1700 RPM. It even does it while sitting still in gear. The funny thing is, it does this only in gear( Park and neutral do not stutter), which lead me to believe it was an issue with the lockup solenoid for the torque converter, or the speed sensor. It also stops stuttering once the transmission has warmed up(the clutch packs, valves, bands, and of course the fluid, possibly the issue?), NOT the engine. The stuttering is especially pronounced in cold weather. So you could let the engine warm up and not put it in gear, and once you finally do, the stuttering is there.

But before I tear into the trans, I wondered if anyone has an opinion on it? The mechanic believes it needs a tune up. The chances of this seem pretty remote. Thank you in advance for any help!