Would need to see the lines arrangement to understand the extra ports. That GE compressor shouldn't have an external precooler nor any other reason for extra ports. It is possible that it has more than one return line but should have only one discharge line. If the original had more than one return line, you can tee together the two lines and combine then into one. However, I expect that once you get the old compressor out, it will become more evident how it is plumbed.
As for the capillary tube, it is indeed difficult to flush these systems. The bigger issue is that the cap tube restricts efforts to flush the old oil from the evaporator, so that will need to be disconnected at the evaporator if possible. Sometimes it is not possible, and the old oil has to stay. If that is the case, it will likely not hurt anything as long as the system is properly evacuated with heat.
In general, if you are keeping the same compressor horsepower, but changing from an R12 specification compressor to an R134A specification compressor you will need to increase the length of the capillary tube. There is more than one method to calculate or estimate this. If you can measure the length of the original cap tube, it is easy to do; but if you cannot access the tube to measure it, sometimes you have to estimate based on the cap tube charts. In general, adding about 10 to 15% length to the cap tube is by-the-book. Often things work without adding any to the tube, but sometimes this is needed. If the system has problems getting cold enough to satisfy the thermostat before freezing back to the compressor, the tube is flowing too much refrigerant or it is overcharged. If dialing in the charge can't get it working correctly, it may need cap tube adjustment. Some of these systems were marginal from the factory and dialing them in is a trick.
Back to the compressor ports, it is absolutely critical that the plumbing is correct. As far as I know, GE never made a compressor that required more than one return port. If it appears this is the case, need to be extremely careful to get a complete understanding of how the system is engineered. There are always things out there that nobody has seen. Recognizing that it is different and needs to be investigated is a critical skill in this field. Pictures will help.