help, odd engine noises

Still pretty new to working on engines. I have never opened up even the valve covers, But I have done a timing chain and gear replacement. Im not afraid to get in there, just not sure what to expect. I have book knowledge, but not much experience. My 5.0 is idleing rough, the rpms drop every few seconds like it is missing. feels slow but pretty strong under acceleration. Makes an odd diesel engine noise along with other quiet ticking and clunking noises. 121K miles on the stock engine with CAI, catted X pipe, and catback. Dont have the money for HCI rebuild that i plan on doing myself right now and im sure the motor has many more miles in it. I know i have atleast one exhaust leak at the EGR tube, but the noises are more than just that. what should i do? If i open up the valve covers should i just make sure everything is atleast snug, cause it sounds like its coming apart. Im about to go on winter break so ill finally have time to take care of a few problems on the car. Doubtfull, but if anyone is in the Phoenix area and could listen to the odd sound it would be great, but online advise is awsome too. THANKS

I have a bassani catted x-pipe. I have done the whole tune up thing before without much change, but its been a year since, so why not. Think im going to have to wait till I have $400 for some ceramic coated BBK equal length headers first, they come with a new EGR tube dont they? because I have already tried tightening the header bolts down and it didnt stop it completely just made it stop clapping against the block under acceleration, if im gunna get in there to replace the gasket then I might as well do the swap and I dont even know what to do for the EGR tube other than maybe dab some muffler sealer on it, but I might try it cause I cannot afford much right now.