Roy,
My last truck had a Leer Tonneau cover which was excellent at keeping the bed dry but as you stated it was a PITA because they only lift so high and you loose some bed width from the lifting linkage.
I purchased the BakFlip F1 for my current truck and it is fantastic, it mounts very easily and so far has been very watertight, only a couple of drops of water around the tailgate. He advised that you have to install two drain tubes to allow the water to drain from the rails but it is not hard, but if your truck sits on an incline in your driveway, make sure you install the drains on the low side.
What i like about the Bakfip design: 1. you can fold it up part or all of the way; 2. When it is closed and you close your tailgate your items in the bed are secured, you can't open the cover unless the tailgate is open; 3. When i had the hard tonnuau cover if you wanted to get something out of the front of the bed you have to crawl on your hands and knees and to get to the front of the bed, with the Backflip system you just fold up the top as you walk forward.
I researched the Roll-Up metal systems and really liked the idea but i read some posts from users that ran into issues with them freezing up during the winter. If you live in an area that doesn't get a lot of rain/Sleet and then freezes it is not an issue, but they said that if you get rain that fills up the slots and then it freezes before the rain evaporates it would freeze up completely and you have to take it into a heated area to thaw.
Ford's OEM cover is actually the BakFlip F1 and they charge dearly for it (approx $1400), the Backflip comes in 3 different versions (SD, HD, and F1) basically the diffences are the material used on the skin of the cover and it's ability to withstand impact. I purchased the F1 due to it's dent resistance over the other two and it's ability to reflect heat and keep the bed contents cool. I purchased mine from the following website:
BakFlip F1 Tonneau Bed Cover 04-12 Ford F150 Pickup Truck Short Bed 5.5' (66") | eBay
They are basically a internet middleman, you pay them and they have the unit drop shipped from the factory, mine arrived in 3 days.
If you have any questions, please let me know.
Dave