OK -
The T39 raises the effective impedance of the 3012LF from 8 ohms to 10 ohms - and the 3012LF is rated for 450 watts. So on the subwoofer side of the amp you won't want to exceed 67 volts - but to be on the safe side I'd keep it to 60 volts. Follow the instructions you can find elsewhere on the forum for using a voltmeter to set the limiter. Since you're stuck with limiter settings of -3dB, -6dB, and -12dB, I'd probably err on the side of caution and go with the -3dB, which -should- keep the amp limited to 51 volts on that channel, but never trust the specs - use a voltmeter and find out for yourself what -your- amp does. Without the limiter engaged that amp is capable of 72 volts (at least on paper), which is more than enough to cook your drivers, regardless of the additional impedance from horn-loading.
For the OT12 side of the amp you're looking at the 3012HO - 400 watts at 8 ohms, or roughly 56 volts. Again, test it out with a voltmeter using a frequency within the passband of the speaker, but I'd hazard a guess you'll probably wind up using the -3dB setting on the limiter.
As far as the crossover, you've got the HPF for the subs right where it should be - 45hz is what bill says for 2 or less T39s, 46hz is a little extra padding on the safe side. Although I've never used an omnitop, I've heard several forum members complain that they tend to run out of "oomph" in the low end when they're crossed to low, so I'd think about crossing between the cabinets at around 120hz instead of 100hz. The T39s should be fine that high. Of course, the crossover point between the cabinets is entirely up to you, and I've always found that it's better to play around with that and use your ears to find the sweet spot.
For EQing, try not to do too much EQing in the amp's processor - don't eq to taste, just EQ some of the idiosyncrasies of the cabinets out. Here's a chart of your two cabinets below:

(Note that the T39 is the wrong width, and the OT12 doesn't say which driver it's got... so these charts aren't perfect)
The first, most obvious correction you'll want to make is to EQ the T39 to tame some of that rising response out of it. If you set a PEQ at the PDF frequency with a fairly wide Q and bring it down 6db or so that should bring it back in line with the OT12s. (alternatively, you could just adjust the LPF downward a bit, say, to 110hz, and then set the PEQ to -3dB or so. It might actually sound better that way as you'll get less of the highs in the subs.) Other than that there's some adjustments to do to the OT12, especially in the high end, but in order to do that properly you'd really need a good graph of what -your- cabinets are doing. If your response chart looks anything like the above, a good starting point would be a PEQ at 8 khz with a medium width set to -3dB or so.
You asked for my input, so here you go.
JOHNb
Low End Junkie for over 20 years.
4 DR250s
4 Tuba36s @ 30" wide
2 ATs
...and a very serious addiction to the smell of BB sawdust and curing PL.