“…. I've done the timing belt before. I'm starting to wonder if it could have jumped a tooth or something. If the balance shaft wasn't right that could account for the vibration I'm seeing at idle…”

On your engine the timing of that third shaft (I-shaft) is not critical as all it does is drive the oil pump. It doesn’t act as a balance shaft as on the 16 valve engines. However, if the cam timing is off it can cause the symptoms you describe. It’s easy to check by removing the upper timing belt cover ONLY and comparing the cam timing mark position to TDC on the crank pulley. This method only works if the outer ring of the damper pulley has never spun on the inner part of the pulley. Your 88 may not even have the rubber isolation ring type of pulley, in which case this “spinning” could not have occurred and the crank timing marks CAN be relied upon to locate TDC. If the the damper pulley timing marks are suspect you can pull the #1 spark plug and, with a plastic straw, “feel” the piston up to TDC. It’s not very exact but if TDC on the damper pulley appears to closely coincide with piston TDC then it’s a safe bet that the pulley has never spun.
Also, when setting the cam timing mark to TDC, be careful to not mistakenly align it to the little circular mold mark in the front edge of the rear belt cover. That would put the cam about three teeth out of time. I made that mistake once. The correct mark is back inside the rear cover where a tall person needs to bend way over to see it.

Did you say you had a timing light? What is it indicating as far as ignition timing?