Yes any engine with 99H prefix is/was originally a 998.
Might have a 1098 crank if someone's been in there- to check put a pencil in thru a plug hole, turn the engine by hand. Put 2 marks on the pencil for TDC & BDC.
If marks are 3" apart it's got a 998 crank, if 3.3" apart it's a 1098.
To rebuild a Mini gearbox
properly,with all new synchros, bearings, layshaft and a comp diff pin (good idea) will cost around $750 just for the parts. So add haul it out, fix and refit you are probably right on costs.
Often the synchros (except 2nd) are good, if so at $30+ each, I'd keep them.

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DrMini- 1970 wasaMatic 1360, Mk1S crank, 86.6HP (ATW) =~125 @ crank, 45 Dellorto (38 chokes), RE282 sprint cam, 1.5 rockers, 11.0:1 C/R.
