CVP Stage I kit in a 2005 Sportster XL1200C

Hope someone can help? I was having problen like almost everyone here with stuttering an coughing back through the carburator when blipping the throttle or when beginning to accellerate form a stop. I ordered the Stage I kit and when it came, I replaced the 42 pilot jet with a 45: Replaced the idle adjustment screw with the EZ-Just screw (original packing). The plug had already been removed from the idle mixture screw tower on the carb body.
I also replaced the emulsion tube, the jet needle, and spring with parts from the kit, but retained the 180 main jet, (Original jet needle was N4NN) and put the carb back on the bike. Now, its really poppin' and running terrible. - - -
Again, I removed the carb and double checked assembly of the top half (diaphram). Everything seemed OK. I replaced the carb on the bike, double checking fit and adjustment of everything. I adjusted the throttle cables as per the Harley manual. This time, I had set the idle mixture screw at two turns open, and backed the idle speed screw all the way out. Turning the idle speed screw a 1/2 turn at a time, I was able to get the engine to fire and remain running. I adjusted the idle speed screw to idle the engine a little above the Harley lope and then a wee bit more.
Now, the engine pops less than at first, but still pops some. The EZ-just screw has little, but some, effect when opened further, but will not stall the engine when turned all the way closed. (no stumble).
A BIG CONCERN HERE: The pipes, especially the front cyninder, get glowing red where they exit the engine, and overall the entire engine and exhaust system seems to be way too hot. The front plug is very black and sooty on the base of the threads; center electrode is black; insulator and ground electrode are white. Rear plug is overall sooty and black with a little deep brown color on the insulator and one side of the ground electrode. NO CHOP plug reading.
My bike is equipped with the Harley Davidson slash down slip on muffler part nr. 80415-04, and the stock air cleaner and backing plate. Mileage is less than 1000. I'm the third owner.
CAN ANYONE GIVE SOME ADVICE? Thanx to all in advance.

Pipes did not overheat before changes were made to carburator. Popping did occurr before changes were made to carb. No exhaust changes were made by me. I bought this bike on eBay with 781 miles on it, and exhaust changes already made.Will change the gaskets, and change to 46 pilot and let you know.

OK Ken, today, I replaced the exhaust gaskets and the muffler interconnect gaskets. I gotta tell you, I was skeptical, but I'm glad you suggested it. The exhaust pipe gaskets were in fair shape, but the pipe installation was botched with the incorrect installation of the muffler interconnect gaskets.
Then, I replaced the 45 pilot jet with the 46. While I was in there, I checked to see if the needle jet was installed right side up. (big opening toward the slide.) I checked for packing in the idle mixture screw, and set it two turns open. I checked the condition of the carburator to intake flange gasket, found it undamaged, and reinstalled the carburator being careful, and double checking my work.
The bike fired after a couple of squirts from the accelerator pump, and it ran a little slow, so I incdreased the idle by use of the idle speed screw. The engine sounded a lot healthier.
while warming, It still coughed a couple of times, and I shut it down without making any adjustments.
Rain here has prevented me from taking a test ride, so tomorrow, I'll test ride to warm up, adjust the idle mixture and idle speed, then install the new plugs and get another reading

OK, a 20 mile test ride revealed the coughing and missing as before. Coughing seems to have moved up into the midrange RMPs. Not so much, but an occasional sputter when pulling away from a traffic light. Coughs when blipping the throttle, but usually on the second or third blip, not on the first.
New plugs read after a midrange RPM shut-off revealed (REAR) base was lightly black except gold where metal showed through; ground strap was grey white and even colored; porcelin was white with a little light grey on the ground strap side. (FRONT) base was the same as the rear, except looking a little cleaner and less black; ground strap was same as the front, but a little less grey, and more white; porcelin was white with a lite hint of grey.
Could this problem be an ignition problem?
Does "cardboard", the sportster guy have any ideas?

I wish to add pictures of my plugs. Can someone guide me?
Thanx

OK - -update: replaced the intake manifold gaskets/O rings and checked for leaks with propane. None found. Went for a twenty mile ride, and motor seemed to run better, but still some coughing out the carburator and an occasional miss while running down the road. Plugs looked like this:

Update: Needed to go to a class abt. 120 miles away so - -ride the bike.
Leaving home 4:30 AM ambient temp about 44 deg F and falling. Bike ran trerrible and would only stop coughing and sputtering when enricher was engaged some. But, I discovered that most of the sputtering and missing occurred at a "slack throttle". IE. when running up on slower traffic and needing to back off some then adjusting throttle to speed of traffic, missing occurred while slowly applying throttle an almost any speed. There was no sputtering or missing when engine braking or when accelerating, or when on a steady uphill pull. On my return trip, I tried to concentrate on what was happening, so that I could relate it here. Same as above, but I noticed a pronounced odor of exhaust, and, smelled like it was not completely burned.
After returning home, I decided to check the plugs, and found an exhaust pipe flange nut lying on the starter motor/ engine case below the rear pipe.
Feeling around the flange, the other flange nut fell off. I remember having torqued those nuts with my beam torque wrench to 120 in. lbs. as specified in the manual. Front flange nuts were loose as well. Here are what the plugs lookes like:

Latest update: Retorqued the exhaust pipe flange nuts to 200 in. lbs. with the beam torque wrench. A 12 mile ride; ambient temp. 58 deg F. Bike warmed up with a lot of coughing and sputtering and bogging on acceleration, but once warmed up, coughing and sputtering reduced to where it was rarely noticable, except as on the previous ride, when at slack throttle. Ie. when cresting a hill, backing offf then applying throttle to maintain a constant speed; or when comming up on slower traffic and needing to regulate speed as above. Throttle on these and similar situations is barely open when coughing occurrs. Throttle is being applied g r a d u a l l y. I can't see a fault in the accelerator pump here. Most, if not all coughing occurrs below 1/4 throttle opening. Below, see those same plugs as above post except after this 12 mile ride.
A question here (or two). - - Why check plugs after a wide open throttle chop? nobody rides around with the main jet completely open at wide open throttle!!! Wouldn't it make more sense to read plugs after a normal ride, and cut the engine before idling enough to skew the reading? Here are my plugs after the 12 mile ride: No WOT chop.