Copy/paste from my Twilight Family Tree :

Yes those are similar names, so similar in fact that the equestrian history books actually swap the two around and just flat out assume they are the same pony a lot of the time.

Clover The Clever is a female unicorn pony, she was the pony present in the hearthwarming tale "The Founding of Equestria", having been court wizard and friends with Princess Platinum. She was never a student of Starswirl, but was a powerful and studious unicorn in her own right, and made many magical and scientific discoveries, but many of the larger achievements attributed to 'Clover the Clever' actually came from her Son, "Clever Clover".

Clever Clover was born after the founding of Equestria, and was the student to Starswirl for a time, he learnt Starswirls tricks to inter-dimensional magic and devoted much of his life to finding magical artefacts and locking them away where they would, hopefully, not harm ponies. He is the reason for a lot of the magical items and anomalies that made their way into the EQG world, having followed the example Starswirl set with The Sirens.

Clover the Clever is based off of a G1 pony simply called "Clover", I added green to her pink mane and tinted her light coloured body towards blue/green instead of purple.
Clever Clover is a G2 Pony, usually called "Prince Clever Clover", I didn't change much about his toy-inspired design, but I did give him a three clover cutiemark instead of a singular one, it also hints at their future relation to Twilight, using the same sparkle.