There was a set of Bestop covers on ebay.

I use the X-bound seatcovers ... I got a set for my 2dr, and then a set front AND back for the 4dr ...

They aren't totally waterproof, but dang close ... they are a very tough canvas cover that will pool water/mud (ask me how I know) ... in fact this afternoon, I need to pull mine and hose em off.

One thing I really like is they have pockets on the seatback (and front/sides) that make a nice place to store some items (maps, TP, spare hoses, clamps, first aid kit, etc). It keeps those items outta the mud/water that gets to boxes and such under the seats or on the floor.

here's a link (I got mine at a local shop for around the same price).
http://www.stylinconcepts.com/parts.aspx?partfamilyid=1320&subcategoryid=232

here's some pics ...

the 4dr rear ...


the 2dr dirty fronts ...


and what's underneath ...


The bench seat in the rear was way too wide, so I sewed up about 4" in the center. I think I'm going to also make a cut so I can get the split back to function again also ...