Cleaning the rack?

Okay, you've got me on this one. I've had two popups covering almost 15 years and never had a problem with the mechanism. No dirt, metal shavings, nothing but an occasional piece of lint. Clearly you're doing something I'm not and I even had a big A/C up there. Are you trying to open it without unlatching? if not, then I would say you're either overloaded or you've misaligned something in your 'cleaning'.

I never really solved the issue, but went at the rack with Q-tips and oil, and it does work better. But if a hard lump, like a tooth of the pinion gear, breaks off and gets stuck in the rack, it is a huge problem. You cannot get the top either up or down. It is not possible to enclose the rack & pinion more than it already is because the traveler has to slide the full length of the rack.

Okan-Star has it just about right in saying it is a weight issue. I use the Apex differently from most, always carrying one canoe on the roof and sometimes 3. Some of you may remember the Outfitter web site which showed the roof going up-and-down with an ATV sitting on the roof. Three canoes weigh less than an ATV. A canoe weighs less than the air conditioner, which is also on the roof. I've tried several methods for raising the roof with that extra weight up there, as the hand crank won't do it. A couple friends pushing up was the most commonly used method. But I constructed 2 air bags from the coated fabric used to build rafts, stuck those on opposite sides of the bed, and hooked them up to the 12 v air compressor. It takes less than a minute, and less than 10 lbs air pressure, to raise the roof by 15 inches or so, and after that, the hand crank easily completes the task.

I don't have a popup, but I think accumulating dirt, oil, metal shavings, means you need a cover for the gears to keep the materials out of it. When up, I think it would be fairly easy to put a cover around the gears to protect them.

I think metal shavings suggests you need to clean it after initial break in and/or use a different lubricant/grease. For other similar mechanisms, I've found that making sure they are tight and in alignment helps.

I don't think its a cleaning issue , its a to much weight issue
I don't know how your camper is optioned , but the one I had and got rid of -had a polarcub , upper cabs , solar , sat dish, luggage rack -never put anything in it . Ordered it new , asked Bob about the lift system and if it was ok with all this and the extended cab roof , he said , it was , it wasent .It bent the arms coming off the heco system , ate teeth , destroyed lift cranks . I have had 2 northstars with that system , no issues . I called heco , they said it was not rated for that much weight . Bob said he could put torsion in the front , may help , at the time they were developing the electric lift , he said he could put that on . After retuning it for a blowen out basement to Colorado , and other issues I sold it with Bobs help for a 7 thousand dollar loss , the new owners didn't know the prob but were being pushed twards a power roof .
I found if you push up with your back to help the roof raise for the first 4" or so it takes a lot of the weight off the system and is easer to lift , I also kept a bag of spare parts with me and a few extra cranks