You can swap just the longblock from a 92 into a 98 without any problems. The only issue I can think of is that you'll need to put a 1/8 NPT pipe plug in the temp sender port at the back driver corner of the cylinder head to keep the coolant in, or just leave the sender in there with nothing connected to it.
As for the manual swap, you will need to either swap the dash+stuff, or pick up a late model manual pedal box/assembly. You will also need a late model ECU for a 5 speed IF you care about the check engine light being on, else you can jumper the NSS and call it a day. If you're picky about the interior looking right, you will need a shifter boot and the plastic bezel trimpiece that holds it in from a late model. If the 92 has the same rearend (8.25 vs d35) you can swap all the linkages and the transfer case plus driveshafts from the 92 into the 98 without issue. You'll want the 92 trans crossmember and bracketry as well.
You should be able to keep the electronics from the 98 without any real issues, aside from a CEL due to the TCU being unhappy about no AW4 present. If you can get it reflashed or buy one online that's set for a 5 speed you can avoid that issue entirely.
So basically -
swap 92 longblock, attach all 98 accessories and sensors
swap 92 transmission
buy and install late model 5 speed pedal box and master/slave (you will need to either adapt the lines or convert the 92 transmission to external slave cylinder, which is an upgrade anyways. internal slave cylinders suck!) OR rework the firewall and swap the harness, dash, steering column, HVAC system, etc. I'd get a pedal box, personally.
swap 92 transfer case and driveshafts (front from 92 will work, rear will work if the 92 and 98 both have the same rear diff), trans crossmember (install 98 VSS sender in 92 transfer case, unless swapping dash/electronics)
buy and install a late model transfer case shift lever and bezel plus a late model shift boot and bezel if you care how it looks. The sheetmetal blockoff plate that goes over the trans tunnel under the console should be the same or close enough to the same on 92 and 98, iirc. Just line the hole for the shifter up properly and screw it down, it's held down with self tappers from the factory.
jumper NSS P/N terminals or connect to the clutch safety switch for the late model pedal box if you care
I think that is about it.
edit: the exhaust bushing mount at the trans crossmember is different so plan on buying a new round-hole style rubber bushing and installing it in the crossmember adapter bracket from the 92 (which came with a half-moon style rubber bushing.) I believe the part is available online for around $3.