to understand this, you have to remember the 'roots' of the tenere: she was designed to win the paris-dakar rallye. the ignition is capacative discharge type, the ignition voltage is produced by a seperate coil in the alternator (cables red and brown).
advantage: ignition is independend from battery, so you can start and ride even with flat battery or you can substitude the battery against a capacitor (as yamaha still does in the latest TT600R).
but long run experience has shown that the isolation of alternator coils wasn't very good in those first years. it is a very common fault in xt600 up to '89 that ignition problems occur because of burned coils.
the cdi unit was build from relativly 'primitive' electronic components, lots of resistors, diodes, capacitors etc. again, sensitve to alternator malfunction and also a source of ignition problems.
so, in 1990 when the 3TB was introduced, yamaha changed the ignition system to an more advanced battery type ignition with tcdi unit. it works perfect, but now a good battery is must. only in xt600k (kickstart version from '91 to '94) the old ignition system was still in use.
isolation of alternator coils is much better since then.
although it is possible to fit a kickstarter in a XT600E you might find it very difficult to kickstart the cold engine. reason is the primary ratio (gears on crankshaft / gearbox axle) which is different from before. yamaha has changed this '88 in tenere 3AJ which was the first tenere without kickstart. you simply cannot revolve the crankshaft fast enough with the kickstarter to start the cold engine. but a perfect carb setting might help, try it.
there are also other differences between the ignition systems, i have pointet out only the main things. in '96 cdi unit and wiring system had been changed again.

check also the chain alignment, gearbox axle of e-start engines is 10 mm longer then those of old k-start engines.

regards
klaus
(you are lucky that i broke my leg, so i have plenty of time to write all this...;-)