So I am not much of a UL guy, but I would like to put together a solid list of gear that I would be taking on this trip. Any feedback would be greatly appreciated.

Also, this is my first time backpacking in this area, so any inside knowledge would also be appreciated.

Footwear:
Oboz Firebrand
(was considering Patagonia Nomad Goretex, for ankle support)

Backcountry.com Merino Trail socks


Clothing:
MHW Xenon Jacket
Patagonia Nano Puff or Down Sweater Hoody (Which one?)
Patagonia Long Sleeve cap 1
(was thinking a Wool 2 T instead)
BC.com Powerstretch Tights

Other Considerations:
Have an R1 Hoody, R2 Fleece and Ascensionist softshell that I would like to put in somewhere. Any feedback would be appreciated.

Gregory Z55
MHW Skyledge 2.1 Tent
MHW Phantom 32 bag
Kleen Canteen 40 oz
Steripen
Camelback bladder
First Aid kit
Beanie
Jetboil Flash
Food (how much should I bring?)

Other questions: Would you suggest I get a packcover? Also, any suggestions on a good sleeping pad [is the Neoair THAT good?]

Much thanks.

Unless you are doing some snow climbing I wouldn't see why you need the Xenon jacket a fleece and/or a softshell. When is your trip?

A down sweater if it's cold and a lightweight rain layer if it's rainy should be plenty.

last week of June.

The Xenon also doubles as my rain jacket (my rainshadow bit the dust).

The San Juans may still have some snow on the higher elevations in June-- so I would try to find more information about the ground conditions closer to the date and be prepared for that possibilty.

As for clothing, I would take your Cap 1 and R1, along with the down sweater and a rain jacket for your upper body. If you have one, then add a windshirt also. Lower half, just some Cap 1 or Cap 2 weight baselayer pants should be all you need for June/July. If you have rain or wind pants then you may want to throw those in your pack also, but if not then don't worry about it. Don't forget a warm hat and warm gloves, along with a sun hat too.

I don't use a Steripen of any kind, but due to what I have heard about them, you may also want to take some MicroPur tablets as back-up.

I would leave the Camelback and Kleen Canteen at home and just take a 2L collapsable, wide-mouth Nalgene bottle with one wide-mouth Gatorade bottle to use with the Steripen.

I would switch out the Jetboil in favor of an alcohol stove.

Food-- general rule of thumb is 1.5-2lbs of food per person, per day, but it really depends on your cooking tyle and eating habits. Some people like more gourmet meals, others just freezer bag meals, energy bars, nuts, dried fruit, GORP etc.

Pads, I get by with a Ridgerest or Z-lite. I personally believe the NeoAir is overpriced for its usefulness. I purchsed one, ended up getting cold in the low-to-mid 30s and now it is back at REI, but as always YMMV.