In all honesty don't worry about the IC right now. It isn't going to hurt anything, it's just a mess!! Wait until you are ready to do the CCV Mod and then pull everything out at once, clean it, and then put it all back and install the CCV Mod. Did you receive the info I sent you on the CCV Mod? Cleaning the IC isn't going to help if you leave the CCV dumping into it, and dumping a hose to atmosphere isn't the right way of doing the CCV Mod and can be more of a mess than they way Ferd planned it. You can also have problems with the boots resealing after you remove them. You don't want to be blowing hoses every time you hit a grade!! A trick is to spray the inside of the hoses and plumbing, wait for it to get tacky and then assemble, this will help keep things together. But in all honesty I wouldn't worry about it until you are ready to do the CCV mod.
I knew your bypass was shot, that's two members in the last week with the same problems, maybe we are going to have a run on bypass lines. Be glad you caught that now or it would have, not maybe, it would have cost you a trans within the first five hundred miles of your trip!! If I didn't send you the CCV Mod info PM me.
NCH