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That is normal. The housing seals with the o-ring around the inserted part. It throws everyone when they first encounter this design. If you try to pull it down flush all around you will snap the ear from the elbow. The throttle body housing actually helps seat it a little straighter by providing an extension on the casting that can be used to lever against to press the elbow down a little flatter as the bolt is snugged up.

Sorry I can't help you with ideas for the preservation/resurrection of the originals. Many of us really dislike the original rims as too small, too narrow and poor backspacing so they appear tucked under. I am one of them. I respect your desire to preserve the originality, so with that in mind, set them aside for restoration and get some later full size GM wheels and tires for daily duty. There are a ton of styles out there for good prices. The 5x115mm bolt circle is on almost all of the Buick, Oldsmobile, Pontiac and some Cadillac full sized cars for more than two decades. Just a suggestion

Pretty much anything that needs to come apart to remove the manifold only makes sense unless it has been done in the last few years. Bypass hose from the water pump, o-ring for the heater pipe, pcv grommets for convenience. EGR gaskets and cleaning the IAC system is easy on the bench, a good option. Many of these items will come with an intake manifold gasket set. Reinstalling the throttle body and manifold adapter will be better done on the bench too. Those little heater pipes are not fun.