kamil,
the drive shaft out of the 240 auto might be a workable lenth for a 300d manual. a 240d and auto tranny is comparable in lenth to a 300d and manual.
dont worry about it until the engine & tranny are in place. use the lowest numbered differenial you have. either a 240 or 300 manual flywheel will work. use brand new mb flywheel bolts. the three shift conectors will need to be shortened and retreaded.
the adapter plates are on all the newer engines are the same. dont worry about finding balance marks on the driveshaft/ clutch components.
you should cut out off the 300d the engine shock mounts and weld into the 240 body.
you will probably need the water pump housing off the 240d to run the 300d off the 240's cooling/heating setup. converting the heating system inside the car is a pita beyond belief.
use the 300d radiator and just ignore the tranny cooler fittings. switch out the speedometer.

if you arent going to use the a/c get rid of the whole thing. with the compressor and hoses gone it is way easier to work on the engine. take the phillips screws out of the solinoid and replace with hex bolts. it makes reassembly easier if you retap all threads and use anti seizure compound.

this conversion is almost a drop in job. i spent way more time cleaning my engine and tranny than putting it in.

don