Is there anything which can be done to account for the underlyings with no listed option contracts?
Classical options pricing theory relies on the idea that any option contract can be simulated with the appropriate dynamic hedging strategy. Options pricing practice indicates that this is sort-of true. So one thing you can do is synthesize the given options by dynamically trading the given equities.
Another common approach is to trade options in closely related companies, with extra hedges to account for the difference. But, you have a more serious problem here....
You are considering this an "arbitrage" strategy without (apparently) taking into account the key difference between a FTSE option and the component options, namely that the former is an option on a portfolio with correlated elements.
The FTSE option value will increase with increasing correlation, even if individual component volatilities remain unchanged. The two-element version with log returns $A_{1,2}$ and correlation $\rho$ shows why:
$$\text{Var}\left(\alpha_1 A_1 + \alpha_2 A_2\right) = \text{Var}\left(\alpha_1 A_1\right) + \text{Var}\left(\alpha_2 A_2\right) + \rho \sqrt{\text{Var}\left(\alpha_1 A_1\right) \text{Var}\left(\alpha_2 A_2\right)}$$
The value of an option position increases with increasing variance of its underlying.
Thus, a position in FTSE options hedged with individual equity options is considered a long (or short) correlation play, and certainly not an arbitrage strategy.