1-3) PS3 doesn't support external or internal subtitles nor MKV container so PMS have to transcode video and burn subs inside so you can see them.
In this case you can't remux but must transcode(re-encode). It means your CPU have to be sufficient for realtime conversion so it can feed PS3 with data fast enough.
If your buffer in PMS not empty when you are seeing judder, most probably problem is network. Transcoded video is up to 10times larger so 20Mbit h.264 stream changes up to 200Mbit MPEG2 stream.
When you are using WIFI, it is no go without limiting quality/bandwidth. So you have to set bandwidth limit in PMS and also it is good to lower final quality little bit (for transcoded video it is impossible to use "losless" quality and 10Mbit bandwidth limit).
In short: judder is in most cases your CPU or network can't feed PS3 fast enough with data.
If you want to load forced subs automatically you should check this link, quite obsolete but you should understand the logic and and naming convention:https://code.google.com/p/pms-exsport/wiki/FAQ