If your main is not class legal but less than 1.05 times the stock area you have to take an MN adjustment (0.995 * D-PN). If it is more than 1.05 times the stock area then you take an ML adjustment (0.98 * D-PN). A non-class legal sail is always assumed to be faster regardless of its size.
There is no official adjustment for non-class legal jib of same sail area or less.
A boat with a lower portsmouth number is faster, so you want a high number.
If your boat is class legal for Hobie 18SX other than the sails, then I think you can make a case that you should start out with the Hobie 18SX number. If it is not, then you do need to start out with the Hobie 18 number and take an additional hit for the spinn. This makes a big difference.
So it looks like if you start as a Hobie 18 you take an MN and SP adjustment. If you start as a Hobie 18SX you take an MN and JU adjustment. The latter will get you a higher number. You should double-check the sail area of the main though - "same sail area or less" is defined as less than 105% of the stock area.
Did you notice that the TheMightyHobie18 SX (with spinnaker) rates a 71.3 and a regular 'ol Hobie 18 rates a 71.4. There's NO WAY you can start with an SX rating and be even remotely fair.
I'd start by saying the SX ratings seem out of whack - looking back to the 2004 numbers they seem a little more reasonable. A question to Darline may clear that up.
As for how to score and what's fair, I think you will find differences among people who do committee.
Here's my take (as former 18 driver and weekly scoring dude for our Fleet):
As for the boat - if the stick on the boat is a Hobie SX stick, I'd say you can start with an SX rating. The rig and spin is the only difference between a magnum and an SX. The wings are the only difference between an 18 and a Magnum. If the stick is some mast you found that just happens to be the same length, I'd start you from the magnum rating.
If your spin rig is not stock SX, then take a mod hit for the major parts non-stock - ie one for the sail, one for the pole. Got a snuffer? Hit. Take a bonus for the smaller jib, take a hit for the non-stock main. Somebody could quibble if you have the old style wings versus the new style wings, I wouldn't.
I don't believe it's necessary for you start with the boat as came from the factory for the base config for all cases.
F-27 example - there was the "stock" 27 config, then people added the square tops, bigger jibs, transom extension/swim platform and asymetrical head sails, and the F-27 Formula was born. Later boats from the factory came that way (minus the platform). Earlier Boats with those mods simply sail as the Formula, not as F-27s with all the mods as factors, unless those mods don't measure in to the Formula parameters/measurements.
My $0.02...