A quick look through the literature will tell you that coffee is simply not paleo\primal. See here
To make coffee you need the beans, a means of roasting and pulverising them, fire to boil your water, a means of filtering the coffee (or going ala Turkish) and some pots\cups or similar to contain your water and tea. This technology only developed in the last few thousand years so it is not possible for coffee to be a pure paleo choice. Maybe our ancestors chewed on the odd coffee bean here or there. That would only be when the beans were on the plant in season and incidental to hunting and foraging activities as coffee is not a food per se. How many beans at a time? How many days of the years? Answer: maybe none. IF they did eat the beans, then not many and not often. From the coffee drinkers point of view this is the optimistic best case scenario and it is still quite different to the dose a coffee drinker gets: ie a small handful of beans pulverised to maximise extraction of the active ingredient which is consumed one or more times on a daily basis. Coffee drinking is just not pure paleo.
If you do like coffee then it is best to consume small quantities (eg a cup) near start of day.. that way it will less likely interfere with sleep. Consider going for one of the varieties with a moderate amount of caffeine- a smaller dose will be cleared through the body more effectively before bed time. It is a stimulant and so if elimination is not an option then moderation is the next best thing.
My version of morning coffee is as follows. I often have gelatin and coconut milk\MCT oil (medium chain triglyceride oil) for "breakfast". I may or may not have lunch.
The gelatin increases your protein intake a little for the day (ie 5-10g) with a bonus of a bit more of certain amino acids that you do not get in lean meat (not unless you eat the gristle\connective tissue, anyway). The coconut and MCT oil give you some reasonably healthy fats as a fuel. You can miss out the coconut milk and just use MCT but mixing the gelatin is trickier.
Approximate amounts are as follows:
flat teaspoon instant coffee (pick a good brand here for flavour, moderate caffeine, safe processing)
flat teaspoon of gelatin
MCT oil teaspoon + tablespoon of coconut milk
You add the coconut/mct oil and then add a teaspoon of gelatin and mix up to a paste. Wait for kettle to boil and slowly add hot water stirring. You will find the gelatin disolves pretty well.
If you don't like coffee then this works ok with Rooibus tea. Make the tea in a second cup and pour the brewed tea into your prepared cup with the gelatin-mct\cocounut paste in it.
Rooibus tea ... might write some more about it on another occassion.