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This is called "black death" (see http://www.aircondition.com/dsmobileac/blackdeath.html) and can be a real problem, especially if some of it gets caught in the condenser and isn't removed. It can blow your new compressor and clog the orifice valve.

First, flush the whole system out well (see http://www.ackits.com/mastercool/flush.htm). It may pay you to remove the condensor and flush that separately: the parallel tube condensers don't flush well (only the bottom tubes get cleaned out), so doing it separately will remove a lot of sludge. Since you are converting, the orifice tube and the receiver dryer will be new, so they do not need flushing.

Buy an Air-Sept suction line in-line filter for the compressor (see http://www.aircondition.com/article2.htm) at http://www.airsept.com/ac_inline.html and a variable orifice valve (see http://www.aircondition.com/vov/) which you can buy from NAPA. The suction filter will prevent sludge from ruining the new compressor, and the VOV will improve air conditioning performance, especially at idle.
Let us know how you make out.