Besides the HP difference, there are more difference between the B18A1 and B18B1...
90-91 B18A1: 130HP, 121 ft/lbs of torque
92-93 B18A1: 140HP, 127 ft/lbs of torque
94+ B18B1: 142HP, 127 ft/lbs of torque. I think the peak torque may hit a few hundred rpm sooner, but off the top of my head I am not sure.
also, the B18A1 (all years) is a cable tranny and uses a mechanical speedo, the B18B1 is a hydro tranny and uses an electronic speedo.
As for a swap, it's always best to do the complete swap, the ecu, tranny, motor, drive axels, etc. Most prices include all this, and the $3000 should as well I would think. $3000 for a 95 B18B1 sounds about right for the complete swap installed.