Yes, as mentioned above, the CV shaft outer ends are different. And slightly harder to find, since the number of base 4WD Tacomas that used them weren't made in huge numbers.
Another small PITA aspect is that the base Tacomas the manual hubs came on did not have ABS, so almost always (there may be super race exceptions?) if you get donor junkyard manual knuckles, they're not going to be drilled to accept ABS sensors, and there will not be a tone ring. So this will disable ABS if you just bolt them on, and at least on my wife's 96, the speedometer/odometer gets it's vehicle speed data from the ABS, so if that goes off line, no speedo/odo. She initially put a Taco speed sensor in the transmission and wired that up.
The alternative (that she did eventually, and I did as part of the initial install) is to take both your original knuckles and the donor manual knuckles apart and reassemble the manual hubs, with a tone ring in place of one of the washers, into the ABS knuckles. Then everything works properly. And replace the bearings while doing that.
As a completely separate step on mine (part of installing a front locker) I also got the non-ADD passenger front diff leg on mine. Thus removing one potential 4WD failure mode while out on the trail. No more vacuum solenoids, lines, and actuator on the diff.