I had the same issues with my 9900 and put up with it for almost six months. The Cyan was the worst culprit, both of them. However, on some occasions the problem seemed to migrate to most of the colours. I couldn't trust it to do more than one large before running a nozzle check, and most of the time a cleaning cycle or two, or more! Once into October I finally made the call to Epson and arranged a warranty service call. From the first print I made I kept a log of issues with the printer, most clogging problems of course. When I started reading from my list the Epson Tech on the phone interrupted me and set up an appointment immediately. It did however take almos4 days to get a tech out, some confusion on the work order I believe. He brought along a new head and pump/cleaning assembly as well. He installed the pump/cleaning assembly first and then the head. Unfortunately he couldn't get the new head working at all, so he re-installed the original. Did all of the necessary alignments and testing procedures and everything has worked well since. He said the clogging problems were usually taken care of with a new cleaning assembly and in my case he was right on the mark. Obviously I still have occasional clogs, but usually one pairs cleaning cycle does the trick and I'm printing again. I would definitely suggest you make that call to Epson ASAP. They also sent me a Cyan and LtCyan cart(350ml), which I appreciated, since I had spent a lot of ink previously with cleaning. My warranty will expire in June and I'm planning on extending it for two years. I've never done that before with Epson Wide Format Printers, but this baby is different. The tech estimated the cost of that service call to be approximately $2300.00. I think the extended warranty is a good insurance policy, although I'm not happy about the fact that it's $300 more in Canada than in the U.S. No idea why that would be the case, but it is.
Gary