Its been over 2 hours now and its yet to stop raining, this is not only annoying as its causing lag to some degree it also prevents me from finding any enderman. Any clue how i can change/fix it?

Which version of the mod are you using?

It stopped raining- after around 4-5 (real life) hours.
1.0.24 (mc 1.12.2 - sevtech ages)

Weather update issues were fixed in 1.0.25.