They instantly bonded and I have began to hand feed them but every time I try to stroke or pick them up they ran away what do I do?
Hi and welcome!
That is totally normal. Many people think that guinea pigs are natural born cuddly pet - that is not the case. they are prey animals and need to get slowly used to a home environment. Pet shop piggies come from a commercial supply mass breeder and haven't had any friendly human interaction before they are being sold as pets.
If your piggies are picking up food from you, then that is actually really. Picking up is cutting very close to prey instincts and petting when free walking is very much a matter of trust and not something that piggy that is not frozen with fear will let you do until it is very comfortable with you; many piggies would rather you didn't if given the choice.
You may find this link here helpful. The forum guides in there give you an understanding of how things look for your piggies, how prey animal instincts function, how you can work around them and make friends with them in their own language and how you can train them to pick them up, carry them and weigh them safely. Tips for introducing lap time are also included:
Settling In And Making Friends With Guinea Pigs - A Guide
This is just one section of our more comprehensive new owners guide which addresses specifically all the areas we get the most questions and concerns about from new owners together with some vital information to avoid problems in the longer term:
Getting Started - New Owners' Most Helpful Guides
Be patient, allow your babies to get their bearings, establish a new group in their new home and make friends slowly. Trust is a tender plant that needs to make deep roots first before it will grow.
If you want piggies used to handling and a home environment straight away, then I would recommend looking for a good standard rescue with a mandatory quarantine, vet care and pregnancy watch; they are full of no longer wanted ex-pets looking for a loving and committed forever home where you do not have to do the whole work from scratch.