All Koni Yellows have a height adjustment. The spring perch has three notches in which it can be mounted. The SP3s as modified by Neuspeed have 5 notches, and are shorter than stock.

I would say that it's possibly the spring perch position you used was such that it would put the ride height a bit higher than stock. You can take the shocks out and see which notch for the spring perches gives you the desired height, although that does require disassembling everything again to adjust it.