Definitely remove the Transmission Fluid Dipstick Tube... it'll make your life easier. It bolts to a stud on the manifold and pulls right out of the transmission once the bolt is removed.
Start the process of sourcing a new grommet/o-ring for it NOW.... I was able to get one for less than $7 overnight, but you may not have that kind of luck. If you have anything resembling luck it won't be difficult to put back in however, I struggled with it. Here is a brief thread covering my difficulties with that grommet/o-ring:
https://gmtnation.com/forums/threads/transmission-dipstick-tube-seal-difficulties.21212/. While my dipstick tube was out of the car I cleaned it extremely well with brake cleaner, removed all rust with a steel brush and sand paper, and painted exposed metal with a decent high temp spray paint (no recollection on brand). DEFINITELY install the new heatshield with the new manifold as it will preserve the life of the dipstick tube and transmission lines (and reduce underhood temperatures).
As for the oil dipstick.... part of me believes that I simply rotated it out of the way. But I also recall that it is probably the easiest thing to remove during the manifold R&R procedure, so I may have pulled it and set it aside without so much as a thought.
For what it's worth, here's my Exhaust Manifold replacement thread:
https://gmtnation.com/forums/threads/exhaust-manifold-replacment-input-requested.21156/
It's wordy, and there are some attempts at humor and there's an example of bad parenting in there. Almost everything that could have gone wrong, did. But I got it done.