Re: Screw magic, We have Science! It works, bitches![3.5][base class][PEACH]
Craft Tool: should be brought in line with Masterwork tools, which are +2 for 100 gp.
Jury Rig: Not terribly useful.
Right Tool For the Job: Again, not all that fantastic.
Duct Tape and Staples: Potentially abuseable with items that do not rely on stats. Also, what does "stats" mean?
Craft Device: Does the engineer need to have access to this spell, either through a scroll or buddy, to understand how to make a device that replicates it (WITH SCIENCE), or can he make any spell he so chooses?
How many times can a device be activated?
Craft Robot: The ability scores should cost extra to increase, such as needing more elaborate or sophisticated parts.
You also forgot the Robot's Wisdom and Charisma, but I assume they're similar.
Good Things Take Time: Again, not terribly useful unless you're worried about items being sundered, and unless I missed something, you're still stuck crafting nonmagical items at this level, so your items aren't even going to get used.
The class is interesting, but ludicrously underpowered. Other than its two main features Craft Device and Craft Robot, which are rather abusable due to some vagueness, it's little more than an Expert with some ability to tweak the parameters of the (nonmagical) gear he makes. The Expert, at least, can pick its class skill list. Since this appears to be designed for D&D, that's what I'm comparing it to. You may want to look into d20 Future if you want some futuristic d20 experiences... D&D really isn't designed to be stretched that far.
If you insist on using D&D, that's fine, but you'll need to give the class a bit more than simply tweaking their parameters. Hardness and HP of the weapon isn't that big of a deal, and percentages don't work well with most of them, anyway.
I suggest focusing not so much on slightly improving or speeding up crafting, but being able to make things no other character can, such as their robots and those odd devices. Maybe even watch some MacGyver episodes for inspiration. Where wizards always have the right tool for the job, the engineer can freakin' MAKE the tool for the job, on the spot.