I did it. I ripped it ALL back to the beginning of the yellow stripe. I have figured out what I was doing wrong, and now I'm on my way to doing it correctly.
So, for all of those who asked for the pattern, here it is. Keep in mind that it ONLY works for the daisy squares, or squares that have this exact stitch count. The daisy squares themselves should have 27 stitches per side (25 st and 1 ch in each corner), and then I do ANOTHER round of dcs across (with dc,tr,ch1,tr,dc) in each corner. This makes it 31 sts on each side, with the ch1 counting as a stitch for both sides it is a corner of. Hope that makes sense. Then you join the squares however you want - whip stitch, slip stitch, whatever. Next you do a round of sc in each sc and ch of the sides of the daisy, putting a hdc in the join seam between each square. In each corner, it will be sc,ch1,sc.
Now, onto the scallop border.
With background color: with right side facing
Join into any corner ch1 with a sl st. Ch1, sc in same stitch,
Rnd1: sc 13, sk 2 sc, 5dc (shell) in next sc, sk 2 sc, sc 3, TURN. (Yes, turn the WHOLE afghan so that you're now looking at the back side of it).
Rnd2: 2dc in last dc of shell, dc, 2dc,dc, 2dc over stitches in shell. Sk 2 sc down side of square, sc 3 into next 3 stitches down side of square. TURN
Rnd 3: (2dc, dc) around arc stitches, 2dc in side of last sc from Rnd 2. Sk 2sc down side of square, 3sc down side of square. TURN
Rnd 4: (2dc, dc, dc) around arc stitches, putting last dc into side of last sc from Rnd 3. Sk 2 sc down side of square, 3sc down side of square. TURN
Rnd 5: Repeat Rnd 4
Rnd 6: (2dc, dc, dc, dc) around arc stitches, putting ANOTHER dc into side of last sc from Rnd 5. Sk 2 sc down side of square, sl st into next sc. ch1, TURN
Rnd 7: sc in each stitch around, putting last sc in side of the last sc of Rnd 6.
sc in hdc of border round. (MARK THIS STITCH)
Repeat from Rnd 1 down side of afghan, excluding the sc in hdc. Instead, do sc,ch1,sc in each corner.
I DID NOT put scallops on the top of the afghan. Instead, I sc across the afghan. Do NOT break off background color after sc across the top.
Color ripples: Work all in Back Loops Only
Contrast colors: Join CC in first sc of first scallop with a sl st. Ch2. (YO, Insert hook into next stitch, pull up a loop, draw a loop through 2 loops on hook) Twice. Draw a loop through all loops on hook. This is a begdc3tog. (6dc, 2dc in next stitch) 4 times, 3dc, (yo, insert hook into next stitch, pull up a loop, draw a loop through 2 loops on hook) Three times. Draw a loop through all loops on hook. This is a dc3tog. dc into next sc on border (This stitch was marked while making semi-circles) - mark this new dc now.
Continue around, but do a dc3tog instead of begdc3tog on successive scallops. Finish off CC after last dc3tog.
Background ripples: Work all scallop stitches into Back Loop Only
Pick up background yarn on hook from previous sc round across top of afghan. (sc,ch1) into corner. (Begin BLO) sc3tog, (6 sc, 2dc in next stitch) 4 times, 3sc, sc3tog. sc in marked dc of contrast round. Continue around, doing sc-ch1-sc in corners. After last scallop, (sc,ch1,sc) in corner, sc across top of afghan. (sc,ch1) in corner ch1. Do not finish off. Continue with another Contrast round.
End with a background ripple and finish off by doing a sc row across top of afghan. Finish off.
These directions have NOT been tested and might require a little fudging in the corners. Best of luck.