How to bid a job: full web application development

Please note that this is NOT a request for bids; I'm a contractor who received a job that turned out to be dramatically more complex than I'd anticipated (due to my dramatic and foolish underestimation of the full requirements).  I'm just curious how my much more experienced colleagues price out their services.  Links to reputable pages showing industry averages would also work.  It's tough to get a real feel for this, since one person's "free diagnosis and proposal" is another person's "$200 if I touch your keyboard".

This job, just as an example:
1.) Installation and configuration of LAMP on existing server.
2.) Migration of Access database to MySQL (including reconfigure of table structure)
3.) Creation of custom Java applets to automatically import data from connected AS400 database to MySQL.
4.) Creation of custom VBscripts to automatically export MS Exchange data to csv, and subsequent MySQL import
5.) HTML recreation of two massive forms (150+ fields) from Access, including AJAX functionality, client-side validation, dynamic element activity and creation, and ridiculously complex financial equations.
6.) Creation of web-based maintenance utilities to administer users, logins, lookup tables, etc.
7.) Filterable search pages with AJAX returns and sortable results.
8.) Several dozen reports of varying complexity that output to formatted PDF.

It would be unprofessional to divulge exactly what I bid, but let it be said that the job is not yet done and my equivalent hourly rate is already well below minimum wage.  That's probably fair, given how ridiculously past deadline the project currently is.

How do real pros price jobs?  Piece by piece?  Estimation of total hours?  Different hourly or aggregate rate for different specific skills and services in a project?  Price to compete with some sort of published standard?  Magic 8 Ball?