I'm not 100% sure if wooden pallets would be suitable, as I'm not sure what wood they're made from. If you can find out I'm sure people would be able to tell you if they're safe. Timber is safe.
Runaround do fantastic tunnel setups:
http://www.runaround.co.uk/
Cuprinol is bunny safe when dry, and comes in lots of colours. It's great for waterproofing.
A slanted roof covered in roofing felt sounds great
Two floors also sound great, although do be aware that both floors need to be 2ft tall on the inside so that bunnies can 'periscope'. Any hutch should be 6ft x 2 x 2 ft, especially if the bunnies don't have permanent access to a run.
For the bedding/substrate what a lot of people are now doing is covering the floor with non-slip lino flooring, and sealing around the edges with bathroom sealant. This completely protects the floor, and then you're free to either continue using substrate/bedding or what might be easier is having litter trays for the buns. They take to them really quickly as long as they're neutered/spayed, and it makes cleaning out a lot easier. Even if you don't use litter trays, having lino flooring will make cleaning out soo much easier as wetness doesn't seep into anything - it's just wipe clean and so easy. I wouldn't use kitchen tiles as they're very slippy. You can place one in in hot weather for them to lie on but apart from that I'd avoid it. I'd personally also avoid straw except for very cold weather (if at all) as if bunnies eat it it's not great for them nutrition wise - you'd be best to stick to hay as food and bedding really, as whatever they nibble then is good for them
You mentioned you replaced the chicken wire with mesh - that's great
The recommended size is 1 x 1/2inch maximum, and that's galvanised weld mesh of 19g or thicker. If there's any mesh on floor level you want to make sure it's definitely that strong and small. You can easily get 1/2 x 1/2 inch weld mesh on eBay which is even better than the 1 x 1/2 inch. Any cats getting their claws through can really hurt a bunny so anything at ground level needs to be even stronger
For weather protection I personally really like roofing sheets for the top of runs, or plywood screwed onto the top painted with cuprinol. For the hutch in the winter it might be helpful to make some shutters from polycarbonate twin walled sheet just to stop the driving rain getting in, but if your tarp covers it that's also fine! I personally love the clear tarpaulin a lot more than the blue stuff, since it's a lot more waterproof!
EDIT: On the new hutch it'd be great to add bolts. At that height it'd be very hard for a predator to actually get to the doors, but at ground level it's easy for a predator to get into hutches without bolts. And the extra ground level means they can access the upper part more easily too. I personally like the bolts that you can add a padlock to, although I just tend to put a 316 steel carabiner clip on instead - it's hard for predators but easy for humans! You can get them fairly cheaply off eBay and if you get the 316 steel ones they'll last too unlike plastic
