You'll need a 1" MML, SYE, and CV drive shaft at a minimum. As already mentioned, changing the pinion angle will also be required.
There are ways to get by with putting belly up without doing a body lift or cutting the tub, but it will limit how flat of a belly skid you can do.
If I were you, I'd run this skid and transmission mount:
http://undercoverfab.com/transfer-case-skid-plates/68-hd-transfer-case-skid-plate-jeep-wrangler-yj-extra-clearance-carbon.htmlhttp://undercoverfab.com/brackets-and-tabs/78-ucf-lopro-transmission-mount-97-02.htmlI understand the link I posted is for a TJ, but if you call them they have YJ mounts as well. Also, I know it says you need a 2" body lift on the skid's page, but if you also run the transmission mount you can run that skid with a 1" body lift without having to cut the tub. (This is the exact combo on mine if you want to check it out.) When selecting options, I'd recommend you get the 1/4" version vice the 3/16" version.
If you don't want a body lift, you can run their standard "extra clearance" skid with the same transmission mount and get by just fine.
The downfall to this combo is everyone I've read that has it says you will experience more drive line vibrations when using that transmission mount. I can't speak from experience on it, but the idea didn't bother me for my build. Since yours is a daily driver, you may elect to get the "extra clearance" skid, run a standard transmission mount, and a 1" body lift.
No matter what combo you decide, you'll need a 1" MML to make it all work. Stop by, check mine out and I'll show you exactly why.
As for changing the degree of your pinion, it is required to maintain proper driveline angles and to prevent premature wear on the CV drive shaft. There are two ways to make it happen. Simple way is to adjust it with degree shims between your spring perches and leaf springs. Harder way is to cut the perches off the axle, relocate them, and weld them back on. Rock and gearhead can certainly chime in here on which is better, but I feel like I'd just run the degree shims (especially if I thought I was going to ditch the D35 eventually).
When selecting the SYE, I went with the Rugged Ridge Mega Short SYE kit. It was cheaper and installed easily. Its not one of the big names, but the parts all seemed to be quality stuff and I'd recommend the kit to someone else. Like Rock mentioned, it can be done under the Jeep but I'd just pull the case and do it on a bench. This way, you'll also be able to clean it out really good and do a good inspection of everything inside. The mega/super short SYE kits shorten the overall length of your drive train thereby allowing you to run a longer drive shaft. This in turn allows for a better driveline angle which allows you to run more suspension droop without binding the CV on the driveshaft. However, you will not need the shorter SYE (it cost about ~$100.00 more) unless you plan to upgrade your rear suspension for more droop. If you ever think you will, then just get the short set up now so you don't have to buy a different set up later.
To sum it all up, your looking at a 1" MML, skid, transmission mount (even if you don't go with a custom one, replace the stock one while you're there), SYE, CV driveshaft, degree shims/spring perches, and a body lift if you decide you want to run one. You may also consider getting the UCF engine skid while you're placing the order. They offer better pricing when you order it all at the same time. Also, make sure to call and ask for a military discount as I know they will give you one.
I hope this answered some of your questions and gives you a better idea of what it takes.