The best way is don't.  Keep that coolant circulating through the spacer, unless you've eliminated the spacer.  I actually tested this back in the day because everyone thought those lines caused the coolant to heat the incoming air and cost them power.  I took temperature readings both with and without the coolant flowing through it.  I saw as much as a 50 degree lower temperature with the coolant as compared to without.  It turns out the underhood temperature is actually higher than the coolant temperature, and the hotter the day the worse it gets.  People still refuse to believe it, even though you have OEM applications where they use air to water intercoolers under superchargers that do the exact same thing. 

I also tested this at the strip and saw a 0.1 second drop in ET with coolant as compare to without on a 90 degree day.  That's 10HP.  The disparity was less to nonexistant when the weather was colder, but it was never better without the coolant flowing. 

I also think it aids in warm up in the cold the way the heat riser through carb intakes do. 

If you ditched the spacer and need to cap the lines they are 1/4", so you need some 1/4" caps and small hose clamps to do it right.  Its not under a ton of pressure (maybe 16psi).  We used to use vacuum caps, but use rubber, not vinyl.

Here it is fro LMR:

https://lmr.com/item/LRS-9424BA/Mustang-Heater-Tube-Assembly-w-o-Coolant-Tube-86-93-50-58

Fair warning, there have been reports of issues with these tubes leaking on the Fox forums.  When building my 331 I elected to spend the extra money and buy a Ford replacement instead.