Earlgrey - been there, done that - by which I mean I have messed up the reconnections more than once when closing up a camera after conversion - D300, D700 and D7000. Somethimes the stuff looks like it is properly connected, but it isn't. So as you plan to do, I just opened up the camera and went in and detached/reattached all connections and cables. I hope that works for you.
I did, however, manage last year to break two D7000 cams in a row when trying to convert them. What happened was that even though I did wear my little spark bracelet connected to a proper spark mat, I blew out the power board in one body. I have no idea why I did that. Never did figure out what I did to the other body. So off to Nikon they went. Repairs didn't cost me too much, thankfully.
Removing the clip frame and dust shaker should not affect anything involving the lens. After all, the retail conversion shops all remove the dust shakers.
Also noted above was something about underexposure in IR. Your converted IR camera will not be able to meter properly in IR because metering is, quite naturally, made to work for Visible wavelengths only. How far off the IR metering is will depend on the camera/lens, the ambient light of your scene and what IR filter you have chosen. After you use your IR cam for a while, you will get a feel for how you need to adjust the exposure compensation. It could go either way, too. You can see up to 2 stops difference either way in IR.
Hope this helps!
Joefitz - some nice work there. I do hope to see you post a photo or two here in Nikongear's IR section also!!!