Firstly, I guess you're getting a tri-lam as you're getting a seaskin?
1. metal vs ykk plastic zip - I have seen both, any personal experiences I should know?
Both are good - plastic is a little more flexible. Metal has a good track record, but plastic is much better than it was.
2. Warm neck option useful?
No. Especially when you need the neck seal replaced - your drysuit repair person will thank you. Your hood goes over your seal anyways....
3. I am thinking siflex seals for the kubi?
You mean silicone seals? Sure. I would definitely get user replaceable wrist seals, such as si-tech. Its a good investment for if you tear a seal at a dive site. User replaceable neck seals is 50/50. I've had many people love them, many hate them. The neck ring does add bulk, and I have seen the neck ring pop out, and it is harder to put back in place than the wrists. It is handy if you tear a neck seal. Personally, I have a neoprene neck seal and I find it comfortable, plus less likely to tear than a latex/silicone. I have silicon wrists, find them comfy, I take the extra time to don/doff them so they don't rip. Don't rush it
4. I am planning on ordering the kubi ring, and I know you also have to order the glove side separately. Since I am in the us, is there a better place to order just the glove side, instead of having it shipped, since I am assuming it is universal. I check dris, but they only seem to sell the whole thing (including the part to install in the suit.
Not really sure what you're after here... I would only go Kubi for dry gloves with glued in seals, otherwise there are better (in my opinion) options for suits with (for example) si-tech cuffs. Pull over gloves require no extra system, are cheap and reliable. There are a few glove systems, the waterproof Ultima is popular, and one or two of the si-tech ones work well. Stay away from the 4th element ones (notoriously difficult) and the Antares (IIRC).
5. Any reason to move any of the valves? I see lots of options, but having never used a dry suit, I am not sure.
Just get standard placement on the upper arm (Dump) and chest (inflation).
6. Sitech valves vs the standard apeks?
Apeks are expensive for no real benefit. Get sitech. Cheaper, just as good.
7. I already have rock boots from deep6, are the compressed neoprene socks the best option?
I prefer boots on the suit. Unless you're cave diving or penetrating wrecks where you need a lot of ankle mobility, then sure, get socks and rock boots. Neoprene socks tend to get holes, need replacing or patching, and if you're diving cold water, tend to be colder as most people cinch down the laces on the rock boots and squash down the loft of the socks worn inside the suit.
8. I know they say the extra protection (Bum, elbow, crutch, shoulder) is not really needed, wondering if it would be a good investment, or just a waste and add extra weight. Thinking the knee for sure, but not sure on the rest.
Knees, Yes. Shoulders, No. Crotch, yes if you have a BP/W. Elbow... what are you doing with your elbows?
9. Pockets - Thinking the standard bellows on both sides, but open to opinions.
Yes. Pick one or two pockets.
Finally - enjoy your new suit!