(shaking head sadly)
Dyno Jet and their utterly crap kits......................you have envisioned a set up that absolutely runs like crap on that motor. Cutting OEM pipes is a good way to lose 10 horsepower. The pods another 10 so now making as much as a Honda 550 maybe.
If you read ANYTHING on the stage 3 setup it is ONLY for competition and with a header and non-stock engine. The kits don't work well at all on the early DOHC and commonly better without them at all. The stage 3 is for over 5000 rpm only running, ergo, RACE ONLY. Even then it is crap. The needle cut sucks and doesn't work on anything but maybe an 1100.
Can't help with engine not even turning over, could be running rich enough to have already damaged the motor. Or you have killed the battery, carb setup won't touch that.
There is NO tune setting for that setup as it is for a junk motor, of course you see that now eh?
Go back to 2-2 1/2 turns on the idle screws and stock size jets, THEY may be too big as you have killed the flow of the motor by removing pipe and the pods do the same. 75-115 on the jets with a header and if good plugs and ignition it will run better but the pipes the way you got it killed it. You need a close to full exhaust or a cheap 4 into 1 header and a stock airbox. If totally stock then 68-102 jets. Anything bigger WILL NOT WORK!!!! Use Honda jets too, the Dyno Jet parts are not the same size jet even with same number on it, they are bigger.
If you have never adjusted the valves, well, that's an issue all by itself. Nobody ever does and you also see how that works out. You are the typical user, the valves don't seat to leak, bike then runs like crap, then you work on carbs more until it won't even start. How most of them die.
Junk the Dyno Jet parts, they are garbage. I once knew someone who worked directly with the owner of the company and after MANY different custom tune setups the guy admitted that their kit did not work with the DOHC for spit. Those kits go on PLENTY of engines that then never run right, if you know what you are doing you can get all the parts for half off and never touch the kit.
When you go to pods the slides drop to not open as much, that makes the carbs go rich, then you richen more in error and then plugs so wet they foul to not start. The CV carbs have driven thousands before you crazy in the same way, they HATE pods. The slides actually open more slightly lean not rich. If valves not set then the slides drop again when the engine cannot pull as hard on the carbs due to the valves. You want the slides opening as fast and as quick as they can. Why Dyno jet drills them, not to increase power but actually just to get slide back to opening as much as it did before! What does that tell you???? The harder the engine sucks the faster the slides open!
Not trying to be mean but the truth of it all, I used to buy them like your condition for a pittance (stealing really) then rework back to stock to sell a bike that runs to 9500 rpm in every gear.
Rule #1 and locked in concrete--when you go to pods the engines flow LESS air, and then you jet them up to run worse. No way will that ever work. A stock airbox is the first part I go looking for to fix one running like yours. If it doesn't fit your idea of what you want in the bike, well, there will be trouble there. Oops, already there. The engines don't even like the stock airbox with like a K&N replacement filter in it, they run worse. OEM paper filter only.
Adjust the valves to .005", the bike runs longer and better.
Did anyone read the label on the pipes that said modification would make bike run worse? They weren't lying there. 4 separate pipes cut short loses a LOT of tuning there, it even can burn exhaust valves.
Take your own prescribed medicine, you said it ran great until you started messing it up, go backwards. Give up on the direction you are going now, if you don't you WILL be forced.