I converted my HJ61 from Auto to manual back in 2004, best thing I did. (I only bought an auto as it was the right price, had a 12HT and is a VX/Sahara model) Had to change it over as the wife refuses to drive and auto..........
depending on what model you have, early or late...... mine was a late. I needed to change the steel gearbox/shiftercover plate from to a manual one, manual tailshafts, (auto trans is longer) drill holes in the chassis for the bolts for the manual crossmember. (I used an early model x/member)
If you have a good 4x4 parts supplier you will be set, its quite easy to do with factory parts and a bit of mechanical knowledge. you can use an early model petrol or diesel 5 speed, all the same until 89/90 when they made the 1HZ a fine spline input shaft.
you should be able to use all the parts from your FJ cruiser, except you will need a diesel flywheel, bellhousing, clutch and sandwich plate.
Let me know if and when you do it if you need any assistance.
My 60 series rebuild....
http://www.outerlimits4x4.com/ftopic103004.php&highlight=
http://www.flyology.com
2006 CRV Sport (wifes car)