It's probably unrelated to the kicker stuff you fixed, I'd do a compression test before you tear it down. my first 200x had a knocking noise only under load and I just let it go unchecked (stupid) untill the skirt broke off the piston one day trashing the top end. Definately better to find the problem and fix it before it turns into a bigger problem. I'd be leaning towards the top end myself. I'm assuming it ran fine with no noises before you repaired the kicker? Good luck!
'74 ATC70 (stock for my nieces)
'84 ATC70 big carb, race cam, and piped (big boys little toy)
'84 ATC125M
'85 ATC125M
'85 ATC185S (200X carb and pipe)
'83 ATC200X (my first trike ever, avatar pic)
'85 ATC200x
'85.5 Tri-Z 250
'85 ATC250R
'79 CJ7 w/351 Cleveland
'77 XL75, '78 XL125
'88 Katana 1100
'00 King quad
'05 LTZ400