I disassembled and reassembled my i9900 case at the beginning of February. When I did that, I discovered the cause of my non-printing cyan: the pipe to the CMY priming pad had popped off. In hindsight, I could have diagnosed that this was the problem from the slight popping sound when that group was cleaned. I took the opportunity to wash all the sponges and clean up the printer.
Disassembly of the i9900 is tedious, not hard. There are more screws than you might suspect, and sometimes you have to pop something loose, but before you apply force, verify that there are no screws that you haven't loosened.
I could not find a disassembly guide for the i9900. However, Canon makes many of their printers alike so that the tricks and parts they use in one printer are the same as those in another. I found the disassembly guide for the ip4000 to provide enough clues to get the job done:
http://www.druckerchannel.de/artikel_druckansicht.php?ID=1831&ps6=1&print=Drucken
One word of caution, there is a ribbon cable and a ground cable on the right hand side connecting to the right front panel. As you lift the cover, be very careful about the attached cables. It's easy to break the ground cable or worse.
At the same time, I also got the i9900 service manual. There is are amazingly useful tables in Part 2: 3. PRINT MODE that tell you exactly what happens with different combinations of media type (e.g. plain paper vs photo paper vs transparency) and quality settings. Hold on to you hat. Depending upon the settings, the i9900 does uindirectional or bidirectional printing, uses 1, 2, 3, 4, 6, 7 or 8 colors, at resolutons of 600x1200 to 4800x2400 in 1, 2, 3, 4, or 8 passes, borderless or with border! Boy did that single table explain a lot of mysteries. Why wasn't it in the user manual?
The table is fantastic. Did you know that specifying "Other photo paper" means you are printing with only 6 colors (CMYK-PC-PM) and on Red or Green? Or that printing on Matte Photo Paper high quality you are using only 7 colors (no Green)? Plain paper standard mode is only using 4 colors. If you're using nonCanon papers and/or inks, the Service manual is absolutely essential just for this table alone.
Of course the other advantage to the Service Manual is that it tells you how to print out the service mode diagnostic prints and dump the eeproms (it appears to me that your printer has one eeprom and your print head has its own eeprom with its own serial number).
My work with the i9900 convinced me that the printer is pretty simple to maintain (think VW bug) and that it is likely to remain a CIS cult machine for a long time. The printhead in the i9900 is shared with the Pro9900 and other Canon printers so it is apt to be available for many more years. I've been using MediaStree inks in a MediaStreet CIS system in mine for about 4 years. I've had the usual need to clean clogs and required new print head every couple of years. In return, I've had the freedom to print big and often to get the perfect print because the ink cost was low.