SP is Small Pin and BP is Big Pin. It refers to the size of the piston wrist pin, which I think are 20 and 22mm, respectively (I think, I can't recall at the moment if that is their actual size). The SP cases have 10 studs on the intake side, and the cranks use smaller, lighter webs. The BP cases have 12 studs on the intake side and have larger crank webs. SP cranks fit in BP cases, but it is not a recommended combo due to case volume and primary compression issues. BP cranks do not fit in SP cases without a lot of clearance mods-- also not recommended. The SP motors were made from '92 to '94 (I think they stopped in '94, not positive) BP motors went from '95 - whenever they stopped the making the SXR. All BP cranks and cases are interchangeable, but the SXR cases came from the factory with some mild finger porting and a slight change in angle to the intake-- angle change made for more ideal airflow into the cases. Case top and bottom halves should never be swapped or interchanged. They are machined as a matched pair.
The SP motors came with less aggressive cylinder port timings that provide better bottom end/throttle response, and the BP motors came with more aggressive port timings that provided better top speed. The size of the wrist pin should not be a consideration for most engine builds-- the SP cranks hold up just fine unless you are building a 200+psi compression monster. The SP cylinders tend to work ok on BP bottom ends, but I have heard that BP cylinders do not work so well on SP bottom ends. For rec boats, I prefer the SP motors as they tend to be more responsive due to the less aggressive port timings and lighter cranks. For racing the, either generally works fine or can be made to work fine, though the porting in the BP cylinder is more ideal in stock form. Most people don't realize how close the BP porting is to what the Kawi race team ran-- it is surprisingly close. Much closer than the SP or SXR cylinders in stock form-- MUCH closer. All the cylinders, except the early SX cylinder, have a 2 digit stamp in the intake side. 22 is an SP cylinder, 24 is a BP cylinder with terrible transfer ports, 29 is a BP cylinder (the good BP cylinder), and 55 is the SXR cylinder. The crappy BP cylinder was only made in '95. Your '98 should have a #29 on it, unless a previous owner swapped it for something else.
The CDI is the black box with "all the wires" plugged into it. It takes a reading from the pickup in the stator cover and provides the proper ignition timing for the given RPM. The orange and black wires that come from the CDI are plugged into the ignition coil-- this is what provides spark to the plugs. Both plugs spark every 180*. So one is sparking at/near the top of the piston stroke under compression like it should, and the other sparks at/near the bottom of the piston stroke during the exhaust/scavenging cycle, basically doing nothing. Not an important fact, but worth noting. The reason the BP CDI has a better, more aggressive timing curve, was to make up for some of the bottom end lost from the more aggressive port timings noted above.
There should be a 4 or 8 digit number stamped on the CDI-- tell me what it is. Some units have the complete 8 digit part number on them, some were only stamped with the first 4 digits.