Provided there is no difference between the crankshafts for a manual vs auto donk, all should be ok. (Haven't heard of any such thing with the Tdi).
Spend a few hours taking photos of both vehicles, underneath and under the bonnet. Compare, and make a list of bits that are not common to both. (Think things like kickdown linkages, etc.) Also look for any bracketry that is different between auto and manual.
Work out exactly what will need swapping from one to the other BEFORE you start pulling bits out. Not too bad if the vehicles are physically close to each other, but if they're on opposite sides of town, it can be frustrating to be held up because of a missing clip or clevis pin!
Being relatively lo-tech engines, the actual swap shouldn't be difficult. The '98 may have the electronic fuel control on the pump, but that would be about it.
Good luck, report back (with pictures)!
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1999 Disco TD5 ("Bluey")
1996 Disco 300 TDi ("Slo-Mo")
1995 P38A 4.6 HSE ("The Limo")
1966 No 5 Trailer (ARN 173 075) soon to be camper
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