I used to own an SR500, which is a stones throw from the 600 model, so I think I can contribute something here...
Not only does the SR300 have different pickups, but the preamp is also quite different as well. In regards to which one is the weakest link, I can't say for sure, but there are definitely some great pickup options out there if you like the MK-1's. I think the MK-1's are very good for a stock set of pickups and WAY better than the CAP's in the SR400 and below series, but for around what you'd pay for replacement MK1's, you could get a much nicer set of pickups.
I'm in the market for modding an SR305 with some new pickups and a real
Bart preamp in the near future. Through my research, your best bet may be getting in touch with David (SGD Lutherie) on here. He makes a pickup that fits the slot for those and it's much higher quality than the MK1s from what I can gather. David also does customs (though it takes a while, he's a popular guy on here and gets rave reviews) so if you know what you want and would like to improve on with the MK1's he can definitely make it happen.
The ones I'm looking at are a fit for the 4 or 5 string Ibanez SR models: http://www.sgd-lutherie.com/pages/ND3-BC5.html
There are other options, but I think you'll find David's pickups may be the best option for this situation. The price is definitely reasonable for such a set, PM him if you have any questions, he's on here almost every day.