Can someone check my workflow for video editing?

I have a question about my workflow with my Adobe Products.  I'm hoping someone can check my workflow.
I feel like I understand most of this process but I have a few questions listed below.
If someone could please read and tell me where I might be able to speed up my workflow I would be appreciative.
Any help is appreciated!!!!!!!!!
Questions-
• Why do my exports take so long with Premiere and Media Encoder?
• Why does Premier take anywhere from 5-10 minutes to fully load my projects?
• Why does Premier take so long to load my previously rendered preview files?
• Are my settings OK with Media Encoder?
• Why can't I get Media Encoder to export higher than a resolution of 786x524 for MP4?
Computer Specs:
MacPro, 2.8 Quad Core, 10GB RAM, ATI Radeaon HD 5770 1024MB, Mac OSX Mavericks 10.9.5
Software: Using Adobe CS 6 software,
A typical project for me:
Resolution 1000 x 563px, 10 minutes long, to be played/viewed on the Web.
My workflow and settings in more detail:
• I usually start in After Effects then move the AE comps into Premiere and edit with many other clips, then export to ProRes, finally I compress that ProRes file (Adobe Media Encoder) to a variety of necessary formats.
I start with After Effects and create about 20 or 30 projects, each is anywhere from 5 seconds to 30 seconds long.
I start a new Premier Project (Preview Files set to QT, H.264, 1000x563px) and import the AE comps directly into Premiere.Premiere has to render my AE comps but I like the flexibility of being able to "go-back" and alter my AE file, it auto updates in Premiere
I edit all my clips in Premiere, my entire timeline is rendered and has the Green Line.Anytime I close my project and reopen it. Premiere takes about 5-10 minutes to load the project.  Premiere initially opens quickly but takes a long time to link up all the rendered preview files.  This seems way too long
Upon finalizing my project in Premiere I export out to ProRes 422.
Settings For this is: Export Video, Same Resolution as project, Quality 100%, 30fps, Progressive, Square Pix, 24bit, Use Max Render Quality, Use Frame Blending.
For my 10 minute animation this takes about 45 minutes. I feel like that's OK.  My AE clips can be a bit heavy with stills, particles, effete and etc
This results in about a 11GB ProRes file.  Does that sound right?
I now have a fantastic ProRes  copy of my hard earned work.... but I need to encode it to get it on the web, to clients, to friends, to the Universe.
I import this file into Adobe Media Encoder.  I need to get this into 3 different formats, .H264, FLV and .MP4.  This processes usually take about 12 hrs for me.  Seems too long.
MP4 settings: Multiplexer MP4/ Standard, Dimensions I can't get them above 786x524 this is frustrating, Level: Advanced Level 5, VBR 1pass 1,500
FLV Settings: Format FLV, Dimensions 1000x563, VBR 2 pass, Bitrate 1,200, default target rates and Key Frame
h.264 settings: Codec H.264, Dimensions 1000x563, 30fps, Progressive, Square Pix, Optimized Stills, Bit Rate 1,500
That's about it.

You're missing the JSTL JAR's in the classpath.

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