First off, going from guitar to bass there are some things to keep in mind. First, the gauge of the G string on a bass guitar is larger than that of the low E string on a guitar. But, it sounds a third higher, so it's actually tuned to a higher tension. Second, the scale length of the average "long scale" bass is 34", which is a little more than 8" longer than most Fender guitars and almost 10" longer than most Gibsons. That extra ten inches is a lot of room for small changes in relief or shim angle to have a big effect from the nut to the 21st fret. Third, despite the higher tension, the higher-mass bass strings really get moving when you pluck them, so basses need more clearance from the fretboard to vibrate freely, and that means a higher action than you'll be used to with a guitar.
I second the recommendations that you need a real measuring device. Head to a home improvement store or office supply store and ask for one of these precision metal straightedges:
These run about $2 and measure accurately down to 1/64". This is essential for adjusting saddle and pickup height; you simply cannot eyeball this.
Second, you need a gap feeler. This can be had for a the cost of changing one of your guitars' strings; keep the cutting from the high E and B strings. The E will be in the .090-.011 range which is the butter zone for guitar neck relief (measured by capoing the first fret, holding the string down at the last fret and slipping the feeler under at around the 8th or 9th fret), while the slightly thicker .012-.014 cutting off a B string is perfect for bass necks (if you're still ending up with too much up-bow for your tastes, you can go as flat as .010" relief, but you'll start to buzz in the first position frets if you aim for a ruler-straight neck).
With these two tools, do your setup again, using the measurement guidelines for Fender basses (your Rogue is basically a restyled Fender Precision). I think you'll be much happier with the results.
