Hi Rob,
BTW...Welcome to Jeepz.com.
I read the entire thread and thought I would add my $00.02 worth of perspective. Hopefully, I will not walk over already well-trod ground.
I have an OEM hardtop. I think it is of better construction quality than aftermarket hardtops. Just my opinion -- others might disagree.
I find that the hardtop isn't really quieter or warmer than the soft-top. They are both noisy: the soft-top slaps and whistles, the hardtop rumbles. Pick your poison. The Jeep heater is adequate with either top installed.
One advantage of the hardtop during winter becomes apparent when there is 18-inches of fresh, lake-effect (wet and heavy) snow on the Jeep. The hardtop won't sag and permanently stretch under that snow-load. The glass windows of the hardtop hold up to winter temps and road salt better than plastic soft-top windows. The hardtop liftgate is easier to work with gloved hands at 12 degrees-F than soft-top rear window zippers and snap-fasteners.
In my opinion, the hardtop is the safer choice during winter. By way of example: a sport peculiar to snow country is called "ice frisbee." Here is how the game is played: you drive at 65-MPH behind an 18-wheeler on an interstate highway. You wait until a manhole cover-sized sheet of ice peels off the trailer roof. You then watch the ice frisbee sail, soar, flip in the air and fall toward the ground, and you catch the ice frisbee on the roof of your Jeep. The ice frisbee game is best enjoyed in a hardtop equipped Jeep.
As regards hardtop storage and installation, I put together a lifting system using a ganged-pulley rope hoist purchased from Harbor Freight. I can remove or replace the CJ hardtop, working alone, in less than 30-minutes. The hardtop spends the summer in the garage, suspended from the roof rafters. But, we have high, peaked roofs here in snow-country, so I can hoist and store the hardtop high enough above the garage floor to walk under the hanging hardtop. The hardtop is safely stored and does not create a walk-around nuisance. Total cost: around $20.
Roofrack: You might want to do some measuring. My CJ (lifted by 3-inches), with hardtop, clears the garage door opening with only 3 or 4-inches of vertical clearance to spare. Add a roofrack, and the CJ might be too tall to go in/out of the garage. Your situation, of course, might differ.
I hope my thoughts prove useful.
Regards,
Gadget