Creating a post on this as I really struggled to find any information online at all but it is very easy.
I am visiting Peja, Kosovo (also known as Pec but locally people seem to call it Peja). Hiking in the Rugova valley is one of the main reasons for being here.
There is a daily bus that starts in Peja at 8am and 3pm and drives up to Boge, stopping at trailheads along the way. It returns at 9am and 4pm (no set time for the lower trailheads, just when it gets there).
It starts just outside the Peja bus station, outside the Dielli bakery, the driver did look around the station itself for people that looked like hikers before leaving. As I understand it only runs in summer, but is running as of early May. In peak season tickets are 5eur, out of season the driver will split 40eur between the number of hikers (which I think is fair, and works out cheaper than paying 35-50eur for a taxi).
I hiked from Kushinqe to Leqinat, which I think is the most popular route. It is currently very snowy and I would take the hike seriously, its not a tourist track right now, but is probably manageable in summer for most who have planned to visit a hiking area.