I've recently cut to top off of my 2 door cherokee from behind the driver seats to the back. I was looking to put in a roll cage just for added safety. Does anyone have any experience with the bolt in roll cages?

How much of the roof, just the skin or down past the gutters? As flimsy as the roof is, it along with the pillars are a structural part of the jeep.
If the roof is gone than I believe a cage will be an absolute necessity and will need to be welded into chassis plates/frame stiffeners.

adding a weld in cage would be the safest and strongest bet removing the top on a uni-frame vechile will weakin it alot. if you did frame stiffners and a weld in cage the jeeps performance and safety will be alot better.

With you cutting the body i would have a full cage welded in 6 point minimum.

imagine your jeep as a cardboard box. now bolt a cage into this box, but the cage only bolts to the floor of the box. you've still got 3 planes that aren't utilizing that cage. now chop the roof off that box. starting to sound pretty flimsy?

a cage integrated into the roof, frame rails, and possibly even the pillars is the only way to go. bolting a cage to your floor? sure it does something. but in your case, something is no where near enough

Do you have any 4x4 shops around you or a chassis shop that builds race cars?Talk to both see what they will charge you to make your jeep safe to drive.And please don't drive it tell you get a cage in it.