I think having the live set in one project is what most people do, if they want to have them on the beat all the time, as you don’t have the ability to move the playhead around like you do on a turntable.
Having an external clock alone won’t resolve the issue of having to hit play in time, as a clock is just a fast and regular pulse and has nothing to do with song position.

The problem with mixing up parts from several songs is the reason people use loopers or additional samplers in their liveset. I use an OT in „the middle“, so I can quickly sample a 4-bar loop of what is currently playing and prepare/switch to the next song without the old one beeing interrupted and than use the Crossfades to slowly move over (or blend in) new parts until songs changed.

What you could also do is check if there are midi tools out there that might help (or if you are able to; build one your own).
As far as I understand, the E-RM midiclock does exactly what you might need. I you know a little bit about arduino, building a small box that does cue up midi-start comands to the next bar isn’t that big of a deal either.

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