Needless to say this is a game that was sorely under-promoted by Eidos; much to their shame as there's enough quality and attention to detail in it that it's clear the developers at Backbone Entertainment cared about putting out a good game.
Here's some general advice for new players. Email me your tips and I may include them, and be sure to give me your code if you want to duke it out. Mine is located at the bottom of the page.
1. On the topic of part-making and experimentation. Part quality relates directly to the strength of attacks and to the amount of damage a part can take. Defects or enhancements are imbued by secondary ingredients used, though there is no one-to-one mapping of each kind of defect or enhancement bestowed and you can end up with a different result each time you experiment (i.e. you'll still get a defect, but maybe a different one if you redo the exact same experiment). So, just because the same primary ingredient will give you the same part, trying the experiment again with different secondary ingredients to see if you can get a really good enhancement is very much worthwhile.
I would never discount a part because of a defect alone. Some defects you can live with -- provided only one part has them: power drain for example, is cumulative -- and if you made a high level part with a rare ingredient you may not really be able to pass it up easily just because it has the Slow defect or reduces your power a little.
2. Always experiment whenever you can. Sure if you talk to the Mads back at the castle they'll tell you to get on with the mission, but improving your monsters is something you'll need to do as you increase in level and start encountering tougher and tougher wandering monsters and bosses.
3. Observation on parts: I've noted that there seems to be two kinds of parts: ones that can take a lot of damage, but don't dish out much pain and have a low energy cost, and those that put the hurt on, but are quite energy-expensive and are easily destroyed. This very noticable in Torsos, where you find some really really tough torsos in the higher levels which output really minimal amounts of energy, but keep on experimenting because there are some that strike a balance.
You might think that all Level 4 parts are superior to everything else you've made, but realise that the higher level parts are also harder to make. Every lab has some parts that are easier to make than others. The level four biological parts are probably the hardest to make overall, but Cardio Chaos and Stitch-o-Matic have to be the worst. The Astral Rift (for making arms) in the alchemical lab is the only thing that comes close. As a consequence a really high quality Level 2 or Level 3 part can often be a better choice for a biological or alchemical part, but if you're ace at those mini-games knock yourself out!
4. Don't forget the defense! You can create a monster with attacks so awesome that the opposition crumbles quite rapidly, but trust me Baron Mharti's Manor has some real tough hombres guarding it and if you lack a part with a really good quality block, the final boss is pretty much unbeatable.
5. Don't forget the old ingredients! Sure that Caustic Juice couldn't make more than a 1st level part for a long time, but hey, you've got some Neutronium as a 2nd ingredient and wow, look what you can make now!
You can swap out secondary and primary ingredients to see the level of part before you experiment. So every time you turn up a new ingredient of any kind try using it with all the other ingredients you have available. Just because a new mechanical ingredient only makes a Level 1 or 2 part when combined with your other mechanical ingredients doesn't mean it won't make a Level 3 or 4 part when combined with a biological or alchemical ingredient. This will mean shuffling through the different labs with all your ingredients, but no one said being a mad scientist was all field work!
6. And what will you do with 15 buckets of mud? Well Leo Lumiere is willing to do a swap for some nice burlap sacks after you've put Mharti in his place...