Dave, you can render the video and audio separately (in two steps) and then merge the video and audio using MKVToolsnix (
https://www.bunkus.org/videotools/mkvtoolnix/ ) if Handbrake doesn't have that functionality already. That should take care of the sync-ing issues you noticed.
Just throwing it out there.... another way to improve the encoding speed would be to use several computers. (since you have those computers from trash)
* Render the video in Vegas and save it to a intermediary format that's supported by x264 codec. AVI with lossless codecs (as long as that codec is installed on all computers x264 runs on) works great.
* Make the video available to several computers (put it on Windows share or NAS with good network card).. or just copy that big file to each computer so that it's available locally before starting to encode... with gigabit network cards copying at 100 MB/s it only takes minutes to copy tens of GB to computers.
* start several computers and run x264 on each computer to encode a part of the big video file
* merge the segments together at the end.
An example of command line x264 to encode a video that's 90000 frames long ( 60 minutes @ 25fps) :
pc1 : x264.exe --profile high --tune film --crf 20 --seek
1 --frames
45000 --output segment0.264 c:\path\to\input.avi
pc2 : x264.exe --profile high --tune film --crf 20 --seek
45001 --frames
45000 --output segment1.264 network_drive:\\path\to\input.avi
--seek and --frames are the magic parameters. seek means start from frame x , --frames means how many frames to encode. --crf tells the quality preset, same meaning as the one in Handbrake.
The number after --frames is just informative, it's the maximum frames to encode, if there's only 15000 frames to encode for example x264 will encode that many and won't complain or stop with error messages, so you can basically script everything (write a .bat file on each computer or something like that) and everything will work fine.
note: first frame may be 0 actually, not sure, anyway it doesn't matter.
So one part can be run on one computer, the other part can be run on another computer, then put together the two (or several) segments.
Separately, you can render the audio to an ac3 or aac file directly in sony software or render to lossless WAV file and use Handbrake to encode to ac3 or aac..
With elementary streams (the .264 extension), it's possible to just copy one file to the end of another and basically you have one continuous .264 file...
With Total Commander ( windows explorer replacement) I simply select the first video segment (segment0.264) and then go in File > Combine files... and Total commander automatically finds segment1.264 and segment2.264 and so on and combines all segments into a single .264 file.
Then you can use MKVToolnix or maybe Handbrake to mux the .264 file and the ac3/aac file together into a mp4 or mkv video file.