Well, take it from experience, when some dude tells you a used 5speed is good for daily driver use.... its probably not. So if you go the 5spd route, rebuild it first or buy one from Marlin. Or be an idiot like me. Im buying one from marlin. Thankfully i only paid like 300 bucks for the one im running now. If you have auto-manual swap questions hit me up! Just messed with all of that in January. You can get Yukon gears for around $200ish, but id take them to someone who knows what they are doing to install them.
Also from experience.... you want a W56B transmission, or at least one that is top shift. Easy way to tell is the transfer-case shifter is coming out of the transfer case. This way, your shifters will sit further back in the cab... I did this when I knew little to nothing, got a G52 and my shifters sit super far forward and the shifters are long as hell. The G52 is for bench seat trucks i believe. Basically if the trans shifter and t-case shifter are right next to each other, it will work.... but it will be super goofy and you wont be able to use the 4runner shift bezel trim and boot. Just sayin