Well I might as well say what I have to offer.
When I got the gun, I was completely amazed by the stock ranges. I opened 'er up and got rid of the AR in the plunger tube, and added a spring. For some reason, it didn't even shoot now. What I think is the problem was A) the rubber head bounced off the front off the plunger tube because it was traveling so fast, and Because of the amount of air, it took the path of least resistance and escaped to the outside of the shell because the AR in the shell was blocking it.
So, obviously I went to go take the AR out of the shell and get rid of that spring. Also, Nerf darts can't fit in the stock shells because they are too long. I wanted to fix this, so I got rid of the AR's (the post and the black disc). Then, the darts were way too loose, so I figured I needed to re-barrel the shells. I busted out the drill press and the 9/16 drill bit and cleaned out the shell. Then I took some 17/32 brass, a couple wraps of e-tape and glued the segments in the shells. I tried it. Sometimes the darts would go launching out of it, sometimes they didn't shoot, and still other times they barely hit the walls 30' away. So they inconsistency has increased, and the range only increased slightly. And I still don't know what's up. I plan on doing a writeup, if only I can get this thing to work uniformly.
There's a mechanism in the gun that pushes the plunger tube forward as the ammo door closes. Did you damage it when you took out the plunger tube? Check the internals directory
Also, when you modded the shells, did you cut through the small plastic circle protruding out the back of the shell? That's part of the seal between the plunger tube and each shell. Damaged seal rings on some of your shells would account for your gun's inconsistent performance.
You can still repair your chain shells without buying a whole new gun:
-buy a refill pack of Buzzbee shells
-pop out the damaged ends of your bad chain shells. I just stuck a screwdriver in the air hole and levered it out.
-cut the bottoms off the new shells to make a patch for the old ones.
-glue the new bottoms onto the old shells with gap-filling Super Glue.