I am glad you asked, because I've been spending a ton of time working on this and thinking about it in prep for fighting MMA. Here's what I've found to work best in terms of setting up takedowns with strikes in an opposite stance situation:
- A great deal depends what angle you're taking, and also your head positioning after your last pre-TD strike. If you're taking an outside angle (most common goal in opposite stance situations), you're probably pumping your jab as you step to the outside. As such, your head will be oriented towards the inside of uke's body. Because of that, your best option here will be a single. I do not recommend changing levels all the way to your knees, though it's certainly not wrong if you have a good single. Rather, I suggest shooting a high single and trying to transition quickly to a bodylock ala Ben Askren.
- If you're taking more or an inside angle, or if you're not angling a whole lot but throwing a 1-2, your head will finish the combo on the outside line and the single will be less practical. From here, I like to shoot a high crotch but one that doesn't turn the corner a lot. Basically you're trying to run the pipe right off the shot. Again, I don't think you need to go to your knees, it's more of a blast style shot. Chris Weidman has had a ton of success with this shot if you want someone to watch.
- Another good option that plays even more off the punch is the knee tap. Throw a few 1-2s to gauge uke's reactions, and if he's bringing his hands up and not moving his feet (pretty common), throw the jab and then instead of following with the cross follow with punching an underhook while blocking the knee with your lead hand. Really try to drive uke over your blocking hand with the underhook making sure to run through him. Dominick Cruz is the master of this TD.
For most of these, you're not really shooting off the punch so much as throwing the punch enough to get a reaction and then feinting the strike into the TD. A key to making this work is really dipping when you throw your jab, because then your jab and your shot entry look very similar and it makes it much harder for uke to read when you're punching and when you're shooting. GSP and Frankie Edgar both make very good use of this type of dipping jab to disguise their shots.
Make sure too that you're actually hitting uke with your jab (at least hitting his guard even if you're not landing clean), shooting from too far out is how Yoel Romero knees you to infinity and beyond. You want to be in punching range before initiating these shots, and you want to have threatened enough with your strikes that uke is bringing his guard high and ideally moving backwards.
One final thing: with a lot of these shots, it's important to not only try and finish the shot but also be ready to just run the guy into the cage and work from there. It's worth practicing, because even if a shot is defended fairly well if you can drive uke all the way too the cage you can often get the TD quickly off the initial cage impact.