Having owned a short-run/production job shop I understand the intricate nature of bidding. We did 1 to 50,000 (or more) and took in anything that came in the door. One thing that was never easy to convey to a new customer, or even many old ones, is that most of the time you'll get a better end price if I just charge time & materials.
When you bid, you've got to add a mystic margin for surprises.
It's an art, though it should be a science, and you've got to be good enough to know how long it's going to take to make a part by breaking it down into operations.
At the old shop rate of $35/hr (yeah, that was a long time ago!!) I'd simply add 5cents every time a piece had to be handled for a second op, plus the machining time.
Figure the number of tools that would be totally consumed (and hope you actually used less), and their cost. I'd buy good quality tools too, so they'd be useful for other jobs. The less you have to add to a job for all the customers, the better. You should also add a small percentage profit into the cost of the tools. After all, the customer is actually buying the tools...he just doesn't get to keep 'em. If the customer DOES keep the tooling, as is often the case with dies and special fixtures, then the percentage is higher.
Same goes for material. One good reason to buy in quantity when you can, so you get a better price, get a better profit, and still save the customer money.
Estimate set up time, run time, and clean up. A lesson from my dad....the customer should pay to clean up his job. Nowadays, there's programming time too.
There's a local job shop that does our overflow or jobs that are beyond our capacity. Just happens that our dad's knew each other back when we were snot-nosed kids sweepin' floors and runnin' the drill press....but anyway...for reference I've checked the prices he's charged for a number of jobs just to see if I've still got my chops up...and

yup. Still in the ballpark!!
All things being equal, and your quality and delivery are good, then too much business and your priced too low. Too little, and ....you're too high, or .....?
Bidding is extra tough these days. For me, it was a fun (and profitable) challenge. Hope it is for you too.
....one screw machine job I bid on we lost to a company that underbid me by 1/2cent/part.
One serious caveat.....
Be very careful on partial shipments!!
There's people who will get you to quote on 1000 pieces, accept that price, take partial shipments, then cancel after they've received 300 parts. They really wanted 300 pieces, but at the 1000 piece price!!