Can I spend Stimhack credits after accessing cards?
According to the run sequence on the back page manual, a run includes "Access Cards", so obviously, one can use the credits from stimhack to trash any accessed cards.

Now, for the Clone Chip part of the question: this is a Paid Ability, so you need a paid abilities window (the green arrow on the path charts) to use the chip.  If you look at the Revised Run structure in the FAQ (last page, here), you will notice that the last Paid Abilities window is 4.3,  which is after passing the last piece of ICE but before any cards are accessed.  So, in your situation, you would not be able to install Crypsis and the 5 credits would be lost.