Nothing like reviving an old thread... I recently acquired a 2nd hand 3800 and it also suffers from magenta nozzle clogging. Y, LC, and PK are slightly clogged but nothing to really stress about. I'm running an all black set. I tried everything except running a cleaning cartridge or doing a nozzle flush by removing the dampers... which I absolutely will not attempt! Printing a digital negative under these conditions results in very gritty mess.
So, with QTR I set it up so that only 5 inks print (3PK, LK, LLK), printed out a negative and it looks pretty good. I'll work this way hoping until Y, LC, and PK nozzles print normally and exclude M entirely... unless it decides to rear it's ugly head!
I sure miss my 4000!