Motorcycle Repair: XL1200C, screaming eagle pipes, stock filter

Question
I bought my XL1200C (2004) second hand at 3000 miles last Spring, and have added 4000 miles to that through the summer.  Now that the winter has arrived it has started spitting back trough the carb.  This prompted me to pull the air filter and jets, and to my surprise, although it has Screaming Eagle pipes, it has not been Stage One tuned, it has the stock filter and jets.  Obviously I will remedy that as soon as possible.  My question is, do you think any damage has been done due to running the pipes with stock jets and filter?  My instinct says probably not as the bikes are running so lean anyway when they are delivered new, but an expert opinion would be very welcome please.  What are recommended main and pilot jet sizes for a Stage 1?
Also, whilst I am very pleased with the pipes, would V & H Straight Shot slip ons run any better?
Many thanks, John.

Answer
Hi John,

I would say no damage has been done woth the running of more free flow pipes and having no jetting to provide the fuel to compensate. Basically, Stage 1 is jetting, stage 2 is usually jetting + pipes, stage 3 being head and cylinder work (depending on the year carb. vs. inj.) In and event, most people would prefer the sound before performance. They need to jet for performance, but hand in hand with the jetting is pipes. If more fuel is added to the system, more exahst will be produced Thus the (free flow) pipes are inevidable.
For your bike since you already have the pipes, for stock jetting I bellieve you have stock #42 pilot jets. You need to obtain a #45 pilot jet. Your main jet will be fine stock, however visit your HD dealer and order part #DW0001 This is a .030 shim. Youll need to put this under the needle to raise it .030 To do this remove the 4 screws at the top of the carb, remove the slide keeping track of the order everything comes out. Slide the needle out of the slide, and install the shim so that the needle is raised the height of the shim. Also make sure you drill out the small brass plug under the carb, remove it to obtain the air/fuel mixture screw. This needs to be turned out 2.5 turns from where the screw is turned into where it seats. not tight, just seated. ok, to review, #45 pilot jet, leave the main, part #DW0001 from your HD dealer under the needle, andair/fuel mixture screw turned out 2.5 turns. I GARANTEE your bike will run %100 better! If your riding in colder weather, it'll need to be different but for now, this should do..the coughing will go away, plus you'll have performance that adds about 5-8 HP....

Hope this helps!

~Mark