Hey all, I picked up a used Hyper a couple months ago and love the damn thing. It's been a dream bike ever since it came out, and my dreams haven't been let down

.
I got it right when the cold weather started to roll in here in GA, so I havent been able to take her out for a good long trip yet (have my Z1000 for that). Plus, I'm a little hesitant without running her by a dealer first to see what kind of condition she's in.
Anyway,I've probably put 2-300 miles on her and it's been awesome the times I get her out. However, the last time I took her out was an unusually cold day (low 40s), I took her to the post office and back...maybe 6 miles round trip. On the way back home she started making some god awful clatter that sounded a lot more like valvetrain clack than dry clutch to me. So I nursed her home, stuck a tender on her and shes been sittin that way for 2 weeks now. It literally sounded like it was out of oil and going to grenade at any second (it has plenty of oil).
I know these are noisey bikes, my first car was a 68 stang I drove for 8 years...so I'm used to noise hah. But, it was weird for me to experience that after things had been warmed up a bit. I'm a guy who starts a bike, smokes a cig, puts gear on then rides off after the engine runs for about 5-7mins when cold.
Edit: 2008 Hypermotard 1100S
Performance and/or response of the bike didnt change...it just suddenly became clacky and noisey as hell, it was one of those subconcious moments telling me to get home ASAP and park her.
Listing the mods that may affect this:
-K&N pod filters from the cycleworks gas tank
-full arrow exhaust
-lightweight flywheel (possibly)
Theres a list of stuff that has been done to it, but those are the immediate pieces I can think of that may affect things.
Bike has about 5,800 miles on it. Judging by the tires the previous owner knew how to ride extremely well...possibly tracked judging from other mods. Typical condensation in the oil sight window from sitting...oil looks decent, going to change it before I ride her again.
I did work at a bikeshop for about 6 years and 2 of those years I was around ducatis...So I am aware of their normal tendencies and the noises they make. This kind of threw up a red flag for me, and I'm honestly scared to ride her without causing more damage. A truck and a trailer is hard for me to come by so are there some things I can check on my own to make sure I'm not going to make things worse before riding her to the shop?