Start by looking at the sparkplugs, they will seldom lie about the air/fuel mixture. In
very rare cases, a very lean mixture will burn poorly and leave rich looking carbon deposits on the plugs. On the other hand, a very rich mixture can wash the plugs clean and look like the engine is running lean.
Triumph silencers are claimed to not need rejetting. BUT, since the engine is setup to run lean anyway, one size richer jets may give you a bit more power.
A slight crackling during deceleration is OK for a high performance engine. Once you get the jetting sorted out and the air injection system is removed, (kit here,
http://www.newspeedmaster.com/html/ai_removal_kit.html ) Adjust the idle mixture for best idle speed and your bike should run well enough to make you smile.