I'll do my best to answer your questions. Someone let me know if I'm wrong.
Yes, you need to flash the Stagefright buildprop to enable JIT and Stagefright.
I don't know but I don't think so.
JIT seems to screw up the Youtube player on some peoples' phones (it has on mine since the VC update, although it worked fine on v9.) I don't know about them making a difference in games but they certainly give me a better score in Quadrant.
Those are pretty normal without Stagefright enabled. Flashing the Stagefright build prop will put you up in to the 800-900 range.
Someone else is going to have to help you out with this one. Above my pay grade.
1. I am curious as to how TR (1.8.3) handles JIT and Stagefright.
a. I see that the ?BuildProp-ThundeROM-Stagefright.zip? is pushed to the sd card after flashing, but do I now need to flash that zip as well in order to enable it?
Yes, you need to flash the Stagefright buildprop to enable JIT and Stagefright.
b. Is JIT in the ?BuildProp-ThundeROM.zip? and does that need to be flashed as well (after flashing TR)? If not how is it enabled?
I don't know but I don't think so.

c. What are your thoughts on JIT and Stagefright; are they needed? I seem to remember reading that they will help with graphics/games.
JIT seems to screw up the Youtube player on some peoples' phones (it has on mine since the VC update, although it worked fine on v9.) I don't know about them making a difference in games but they certainly give me a better score in Quadrant.
d. I ask b/c my quardrant scores are lower than I?ve seen them before (446-510). I know that they?re not as reliable as the Linpack scores, but I think I?m also getting low scores on that as well (MFLOPS: 6.966, Time: 12.04 sec), but I?m not sure.
Those are pretty normal without Stagefright enabled. Flashing the Stagefright build prop will put you up in to the 800-900 range.
2. I have ran into the ?launch day bug? (not coming back from lock w/out holding for options menu) and I was wondering if a ?dirty? flash would require me to reflash the HoneycombS2 theme by jasonevil?
Someone else is going to have to help you out with this one. Above my pay grade.