Ok,
I assume that the bike was serviceable and running smoothly before the alternator failed
So, now the stator and pickup have been replaced but you think that you have a 'weak' spark.
Then we might reasonably assume that the general wiring and the CDI are functioning, therefore the ignition coil might be failing assuming that the coil ht lead and plug cap are not 'leaking' or resisting the flow of electricity

I would next test the coil either by measuring the resistance or by simple substitution
Did you fully charge the battery and did you measure its voltage both on and off load
You can not do any on bike electrical tests without a fully charged serviceable battery
Off load - battery on its own, you should be looking towards 13.5v - 14.5volts
On load - battery connected and ignition on 13v - 13.5v
Cranking the engine over by starter 11.5 - 13v
To start an engine you need;
compression - valve clearances checked but how about the rotational speed of the engine on the starter with the spark plug fitted

is it turning slowly or at normal cranking speed
spark - although there is a spark with the plug removed from the cylinder head the voltage might not be strong enough to jump the gap under compression

I do not know the age or condition of the spark plug but in any case I would fit an alternative NGK Iridium spark plug as they can operate at a lower cranking voltage and are less prone to fouling in my experience
timing of the spark is critical - retarded will not work as the piston will be moving down the bore and so the compression will be reducing - too advanced and the spark will possibly ignite the petrol/air mixture but send the piston back down the bore on the compression stroke thus causing a possible 'backfire'
fuel - petrol and air

is the petrol getting to the carburettor - rough check is by removing the float bowl drain screw, with the control tap 'on' petrol should flow out of the bowl

is the petrol of good quality - replace what is ever in the tank and carburettor with fresh quality petrol

is the carburettor sealed both on its mounting to the engine and to the air filter

is the air filter clean

is the 'choke' operating - check the plunger

does the carburettor need removing for a thorough clean

Off you go back to the workshop and check

Let us know how you get on
TTFN
Hugh.