Motorcycle Repair: 1999 Indian Chief Jetting, intermediate jet, jet size

Question
Hello Gary,
I have a 1999 Indian Chief, Twin 88 with S&S Shorty SUper E Carb, and Vance and Hines Long Shot pipes. Previous owner had added the pipes and a K&N filter. I have found that the main jet is a .070 and the intermediate jet is a .0295. The original stock jets prior to being changed were a .066 and a .028. I am assuming they were changed in conjunction with the new pipes and filter etc. I have been having problems with the bike after it warms up, but only when pulling away in first gear...it will bog out, but only does this after it has been running for about 10 to 15 minutes or so. If I pull away while the engine is fairly cold it runs fine until it warms up. Cold or warm it feels great through all the gears except pulling away in first. I have to overthrottle and ride the clutch a little or it will bog down or stall or die. I am presently replacing my intake manifold seals which are very worn. Previously I tried to adjust the carb but it tends to run ruff at idle and no matter what I did it would still exhibit the same symptom. Hoping to see if these seals were the problem. Can you recommend to me the main and intermediate jet size you would use with this set up. ?? I have been told that I should go back to a .280 intermediate and the .066 anyway. I would appreciate your recommendation on which jets I should be using. Once I replace the seals should I try it with whats in it now or go ahead and install the original sizes. Thanks so much, Pete

Answer
Some times there is no specific jet size stated in the pipe or filter kits. The jets may be right, there is a formula to get close to the jet sizes. Has the carb slide been adjusted? Try pulling out the carb slide and disconnect the cable and remove the needle hanging down through the slide. On most carbs there are 5 grooves at the top of the needle some have 6. Unless the needle is a nail type with only a fixed head,it needs to be adjusted. Try moving the c-clip down 1 groove that will raise the needle. re-install the needle and slide then try the bike again. It may be a little lean in the mid range. The needle is now higher and should allow more fuel into the throat of the carb as you twist the throttle just off idle. I hope this helps.