Have you trained with Gretchen at Dhonal's Keep? The training she offers is great for all characters, especially for the Agents. Your Spellcraft seems to be rather low. Investing in Spellcraft will increase the strength of your spells. Some of the points you invested in Dexterity and the combat skills could have been used for some other skills.
Also, are you playing a true solo Agent, no creations, no help from the NPCs? If you are, the going will be difficult. When I first played Geneforge 3, I played as a solo Agent in the true sense, and had seen the "game over" screen enough times so that it has been permanently seared into my memory.
Some suggestions:
1) Find the stat-boosting items and equip them (Carnelian gloves, Skein of Wisdom).
2) Increase your Intelligence so that you will have more essence and spell energy to cast your spells.
3) Buy as many pods (essence, speed) and gems (icy, spray, etc.) as possible and keep them available.
3) Do not rush through an area, take your time to avoid any nasty surprises.
4) There is no shame in leaving an area, going to a town for a recharge, then returning to the same area and finishing it.
I am sure that other people will give you advice on how to play an Agent. Due to the way I play, I have always found an Agent to be the most challenging...and the most rewarding. I hope this helps out a bit.