1. You don't need to export your TIFF sequence so as to import it into After Effects, you can import RAW image sequence into After Effects directly. Camera RAW will start automatically on importing. What is more, you will be able to change your Camera RAW settings at any time you want inside your AE project: in Project panel select your RAW image sequence, right-click, choose Interpret Footage -> Main... In the dialog box click More Options... button (at bottom left), and Camera RAW opens.
2. Do NOT export to H.264 out of After Effects directly. If you need to export your composition to H.264, export it out of Adobe Media Encoder. Start from HDTV preset. If your goal is to upload your media file on e.g. YouTube, done. If you want to play it back on your computer, but your mediaplayer can't playback it in real time, start to decrease bitrate settings. Keep in mind that modern AVCHD cameras shoot with 28 Mbps, first AVCHD camcorders were shooting with 17 Mbps, YouTube preset in Adobe Media Encoder sets bitrate to 10 Mbps, Vimeo preset - to 8 Mbps.
Choose VBR, 2 Pass so as to benefit from better quality out of smaller file size.
See this The Video Road blogpost on Understanding Colour Processing and benefits of Render at Maximum Depth option.
3. If you're planning to use your After Effects composition in Premiere Pro project, you can use Adobe Dynamic Link. If your After Effects composition is quite complex, render a Digital Intermediate out of After Effects and import it into Premiere Pro. See this discissuon in AE Forum on some production codecs comparison.
P.S. See also this FAQ: What are the best export settings? entry.
First, thanks for the reply. Regarding your points:
1: I skipped the TIF export from Camera Raw and just opened the NEF files as a seqence in AE. So far it works...but why do you think the writer of that video tutorial had us do this? What would be the point? After the video is rendered, it wouldn't matter if the photos were TIF, JPG or NEF right? A rendered video is a rendered video...or am I wrong about this?
2: I started using Media Encorder to do the rendering. Seemed pretty straight forward however my initial problem hasn't been fixed. The video is still choppy. I did a bunch of research on timelapse since my original post and have isolated some possibilities related to exposure time and interval of the photos when shot. However I'm not yet convinced that this is the issue. I've also read up a bunch on bitrates for video codecs and containers. Have a pretty firm grasp of the concepts and have selected values for all that should work.
3: The AE composition is virtually barebones, simply adding the photos into 1080p 24fps. No editing.
Anyways, Im rendering a video right now. If its choppy, I'll put up a youtube link and hopefully can get some more input.
K yeah, here it is....how do I improve this?
...but why do you think the writer of that video tutorial had us do this? What would be the point?
I have no idea of what the tutorial's author intentions were. Ask him, afterwards I will be able to comment on.
After the video is rendered, it wouldn't matter if the photos were TIF, JPG or NEF right? A rendered video is a rendered video...or am I wrong about this?
That depends on how much of the quality loss is acceptable to you. JPG is a highly compressed format with significant generation loss, i.e. you loose a lot with every next render. TIF is a sort of 'production codec'. However, data in superwhites and underdarks may be clipped on rendering. Whether it is acceptable or not does depend on what you are going to do with your footage in post.
here it is....how do I improve this?
And what exactly? The playback is smooth on my side. It shakes at about 0:02, but that has nothing to do with choppiness. Stabilise it.