Discrete toggle flip-flop simulation issue
It's not really a simulation issue I think, more of a circuit design issue. 

You'll need to avoid saturation to get close to 100MHz. Try Schottky clamps on the transistors (eg. A BAT54 dual). The clamp diode is connected from collector to base to prevent saturation. 

Also, you can study how ECL flip-flops work. ECL circuits are more like differential amplifiers and do not have switching transistors that saturate. 

Of course you can simply buy a flip-flop that us guaranteed to work beyond 100MHz such as a NC7SZ74, which will toggle at 250MHz.