On JavaScript part
IMHO, you must not combine all of those and minimize because it wont give you optimal performance always. The trick is to group and minimize the JavaScript files you have. For example, say, you have these js files to loaded in your page
- One (or more) JavaScript librarie(s)
- Some JavaScript files that pulls content via AJAX to your page
- Plugins / Fancy animations / Unicorns that make your site looks pretty cool
- Some js files that does analytics / advertisements
If you minimize all these into one bulky JavaScript file, one wont see any improvement in performance. On contrary, it would be a dreadful experience.
Conversely, if you load them in the following order, it would deliver a better user experience.
- Load the JavaScript libraries from a CDN ( If you use a library that does not have a CDN, then something is very wrong )
- Merge the files that delivers useful content and load them next
- Merge your files that make the site super sexy then
- Load the necessary evil at last ( I prefer the place just above the closing body tag for that)
Even if you have conditional JavaScript files do not worry too much. There are mechanisms in almost all leading programming languages that do it on the fly.
On CSS Part
I am not an expert in CSS and so I cannot elaborate much on that. If you wanna optimize them, you should really use some CSS pre-processors like Sass or LESS or Stylus or something like that.
I am no CSS expert