Probably.
2.9 and 4.0 share the same bellhousing boltpatterns, so the bellhousing will bolt up just find.
With rare exceptions, all BII's, whether 2wd or 4wd used a 4wd A4LD. 2wd BII's had a dummy (13-59) transfer case. If your Explorer is a 4wd, then the A4LD from the BII will have the correct output shaft and tailshaft housing to bolt up to your transfer case. If you have a 2wd Explorer, then you will need to swap tailshaft housing and output shaft (which means dissassembling the transmission).
So, if your Explore is 4wd, the BII's A4LD should bolt in just fine.
However, the question then becomes how good of a rebuild is this. 2.9 A4LD's and 4.0 A4LD's were built to different specs, to account for the extra torque the 4.0 delivers. If this rebuild was a minimal rebuild, or rebuilt to 3.9 specs, it will likely work, but it may not be very reliable. I don't know that I would spend any money on an A4LD that wasn't at least rebuilt to 4.0 specs.