The standard SIII transmission will handle a Tdi without too much problem if it's in reasonable condition, is routinely treated to oil changes (I do it every 10,000 miles) and is frequently checked for correct levels (migration into the transfer box is common as gear many boxes were assembled without any seating compound between the rear bearing carrier and casing). You would need to drive with mechanical sympathy, but that just means using progressive pedal control rather than "binary", heavy footed driving. Feed the power in smoothly and it'll be perfectly happy with full throttle - I have done nearly 30,000 miles with a standard SIII transmission behind a 200Tdi on a heavy vehicle, including driving it around the Alps (including directly up and down ski runs) fully laden.
If you're pulling the head of the existing engine for inspection, then drain and drop the sump too - it'll give you a chance to clean out the gunge, clean the oil pump's strainer of debris, check for bits of valve caps, rocker pads and cam followers (the latter are brass coloured and very fragile), and it'd be worth removing the bearing caps to check the bearings and crank journals (just be very careful to put them back in the same places and orientations they came from). If the journals look good but the bearings are worn, you can cheaply eek out more longevity by replacing just the bearings without removing the crank for regrind - I plan t do just this on my RRC's 300Tdi on its next oil change.