Question what are you using for cabinet decals if you are replacing them.

Yeah, it's mentioned a couple places here. Mine has it.

Yeah, backbox art had a white door, no stars.

You would need an actual Proto ROM, not Preliminary (P-). Which, AFAIK, was never released, and unavailable. In all versions, the "Spiral" mode will catch the ball on the 3rd magnet, but you'll need 9.4H for the Multiball start.

That game is an early sample, your Door light board has space for 4 Door Flashers. Games before mine had 4-Door flasher boards. Mine (or one before mine) started with the door boards with space for only 2 flashers.

It's also interesting that your game does NOT have the missing optos installed. (Clock Passage one is pictured.) My game, built after yours, had those switches already installed from the factory.

They are present in the 9.4H ROM but don’t really do much besides award some points

They registered, but without 9.4H, they didn't do much of anything. (All handled by software, not hardware.) In later samples, they never installed the optos or the wiring, but you can hook it up easily. In early samples, the optos were there and wires to the Opto boards.

In versions prior and including 9.4H, the 2nd Bigkick opto, when activated, just caused the game to try and clear the autofire kicker.
In versions prior to 9.4H, the Clock passage opto did nothing. 9.4H, it awards points and gives a 'tick' noise.
In versions prior to 9.4H, the UR Magnet Opto would score points and activate the magnet during Spira Mode. In 9.4H, those still happen, plus the Magnet Catch at start of Multiball.

I haven’t been able to find any side art that is good quality so far.

Good sample! Keep it as original as possible. Don’t try to make it work like a future pin (for its time). Th value is in the imperfection.

It’s lke any antique...it’s in the imperfection. If you make it look like new, you’ve lost the value.

u sldnt notice any real gameplay difference...id keep which ever tz is in better condition .

Do they still make the clear clock housing?

No. That's what was originally desired for the game, but it was too buggy and had issues. That video was taken from a 'loophole' found during beta-testing for 9.4H. The 'loophole' was correct in the final release, so there's no way to 'trick' the game into doing that. (If some hacker hadn't pissed Ted off, we may have had that in 9.5H.. ) The magnets will only 'catch' balls from the autofire kicker. (in other words, you have to start multiball with only 0 or 1 balls up in the lock.)

Correct. That's the 'Clock Passage' switch.

Congrats on your find. You can learn all about the prototype differences here.

http://gameroomblog.com/features/twilight-zone-pinball-prototype-vs-production

very nice find 3 mag sample thts worth some extra cash

Congrats Hogey! Always a great feeling to run across a gem out in the wild. Enjoy her!

Not Sample *speecifically*.
However, one manufacturer of the translights had some 'stars' without a diffusing backing on them, so they were 'clear'. These translights were used throughout production on random games, AFAIK.