I would remove the tubes and plug the lines, but, do it in a way such that you could put it all back in if you need to.
Here's my reasoning.
1. If you replace it all now, and then someday you do have to pass an emissions test, it may be rusted out again, and may need to be replaced then again. If you don't need it now, don't buy it now.
2. Mine fell out too, and I plugged it up, and still passed my emissions testing here in MA, although that was just the idle test a few years ago, not this new rolling dyno thing they have now. I haven't had to pass that yet - next year. So, I DON'T think not having these parts makes the Jeep a gross-polluter. Plus, your Jeep is already 12 years old. It should not have to pass levels for new vehicles, although I do not know the laws in all states. Here in MA, 15 year old vehicles don't even need to be tested, so I only have a few more years left anyway, at least the way the law is now.
3. Just don't plug up stuff with weld or anthing like that, and you can buy all the stuff then if you need to, but only if you fail, which, if you're tuned up good, and have a good cat, you may not.
4. I have also ditched the BBD, and run a weber carb. This has passed emissions too. Should it have? It is supposedly illegal in all states on a highway driven vehicle. I have asked, through email, the government agency in MA involved in the testing system, and they told me that all they cared about was what came out of the pipe, not what was under the hood. I think this is a good approach. A stock system in poor condition, with all the sensors and vac lines and stuff, with undoubtedly one or more line or sensor or valve broken, will run worse and pollute more than a well tuned vehicle without all that crap. GRANTED, IF the system is new and working properly, it is better, but this is hard to acheive, and probably doesn't stay that way for long. I run a new cat, a pcv, an egr, and the weber.
5. I will never sell my Jeep, so that is not a factor for me. If selling it is in your future, then you may want to replace it all and keep it the way it's supposed to be.
I'm not saying everyone should ditch their pollution stuff, but I'm passing my emissions tests, so it works for me.
Good luck
Pete
88YJ,4"susp,33"BFGMT,9kwinch,homemade swingout,258,999,4.10,weber32/36,GMHEI,one moonguy/wwwthreads_images/icons/smile.gif