About to install apex clip ons front already lowered...

[memper]

The PO lowered the front by about 1/2 inch. I will be installing my clip ons under the top tree. Would it be advised to raise the front back up so the tops of the forks are flush? Rear end has not been raised.

[stopintime]

Not really a simple answer here - it depends on you and your riding style and preferences.

I suggest you get used to riding clip-ons (is quite different) and then decide if you want a higher front end.
Much easier to learn what a mod does if you do one at a time.

If you do it like this - please report back how it turns out

[memper]

Sounds likeva sensible answer.