When I was upgrading one of my A600HDs I installed a IBM Travelstar 4.86GB notebook HD into it. I have KS 3.1. I was playing around and found that all I had to do to make it work with no patches or anything is to simply only partition it upto 4.00GB. So I added like 3 partitions and made sure the last one was not over the 4.00 mark. Works perfectly. Do that and you will be ok.
Oh and I used HDInstTools on Aminet and it allowed me to partition the large drive no probs.