from somebody that has done all three, by far the biggest "seat of the pants" performance improvement is a full VFJ clutch. a tuner really didn't do much for me other than the raising of the limiters tho a slight low end improvement is there. the tuner improvement outside of the raised speed limit is so small that after I drowned mine I left it off and am back to running stock ecu tuning.
my friend and I have basically identical machines and anything I do to mine he does to his, all except for the exhaust which he couldn't find due to MUZZY going out of business. same clutching, snorkel setup, tuners, etc on both machines and mine will just barely pull on him while accelerating, and I mean BARELY. for proof outside the seat of pants-o-meter with tuners on his machine tops out at a hard 64-65mph and mine is a hard 65-66 and will bump 67 occasionally but usually sits at 66 for no longer than I care to run WFO which isn't that long.
FWIW I like my MUZZY but they do get a little loud when youre trying to be quiet and if they go under water and get wet on the inside they are extremely loud, comparable to an HMF IMO
Brett- bought 10-11-15
'15 TERYX T2 LE, stock tires/wheels-for trails, 29.5 Assassinators on STI HD3 wheels for mud, 1" wheel spacers, SATV high clearance front/rear A-arms VIPER Elite 5k winch, Snorkels, Half Windshield, Bubba Rope, CIPA Mirror, LED backup light, APEX Battery, Kawie Billet Shift Handle, VFJ clutch, PC5, MUZZY dual exhaust.