Seperate tip, try turning the game volume down if you're doing commentary, can't hear a word you're saying.
Visually it doesn't seem worth the effort what you're doing though that may be the whole 3D thing. If I just click to watch it on the actual YouTube page it doesn't look good at all - Makes it look like you recorded on 800x600 THEN ballooned it up into a bigger resolution, pixels everywhere. EDIT: I take that back, looks nice at 1080p but seems to be way too much hassle when you could achieve the same results through easier means. Are you playing at that 3k+ Res? Seems very excessive and having to record at that res means monstrously disgusting huge files, must be about 4gigs per 25seconds... I squeeze out 55-60seconds per 4gigs at 1920x1080 - No wonder your compression takes forever
MP4... I never use it... F4V (H.264 codec) is what I use, compresses it nice and small (Setting dependant) and the quality is suprisingly good despite being quite a fast job.
Latest vid is an SF4 vid, a 4 game casual set with a mate. If I watch at 1080p (1920x1080) it literally almost looks exactly how it does when you're playing the game - You physically have to be looking for quality defects to see them.
Only issue with that is the defects are very noticeable when watching on anything other than it's true resolution, but still very watchable - The filzesizes are also moderate, as opposed to small, so slow connections will suffer...
But let's face it, who hasn't got big meg broadband at this stage in time?