Most residency programs can have research built into them, but they are all primarily service driven. You'll at most be able to squirrel away 2-3 months of dedicated research time because you won't be able to stray too much from the base ABP requirements to qualify for the boards. Where I have seen lots of research done, for those who are interested, is at the fellowship level. There is much more flexibility for departments, primarily the really large academic centers, to take on fellows for several years in academically productive positions irrespective of PhD status.
To specifically answer your questions:
- Are these programs generally very competitive? At the fellowship level at brand name institutions, yes they are.
- Do you have to stay in academia? It would be absolutely pointless to go through all this effort in academia to get into a private practice job. You would actually be less competitive for private practice if you spend 1-2 years only doing research and not at the microscope signing out cases.
- Is there any prospect in commercial industry? There are always jobs in industry. But be forewarned that while the pay may be somewhat better in industry, the job security isn't the same as what academia offers.
- I don't know if I have the full resolve to be a principal investigator writing my own grants, but ideally I would want to be part of a larger project and contribute in some way. If that's the case, what's the career projection? When you take an academic job, you either apply for a tenure track or clinical track position. Tenure track is primarily research based with less service work and/or teaching. As such, you will have to secure extramural funding, somehow, to continue to justify your tenure. In general, research funds are drying up across the board and the entrenched players in each field have no intention of relinquishing their share of the pie for newbies. Clinical track is primarily service based with some research, mostly translational, that will be required for promotion(s), etc. Clinical track is becoming increasingly the norm in most departments and most of your salary, whatever that is, will be paid for by your clinical work. You would not want to go clinical track if you spend a couple of years doing basic science research - it would be a waste of time for you and you would be at a disadvantage from diagnostic skill atrophy.
- What about the salary for those types of positions? Can I still make a decent living? The salary is whatever you're able to negotiate based on your academic pedigree and who you know. Most departments I know of start assistant professors at the same salary irrespective of tenure vs. clinical track. The difference is in the source of salary funds. You must scrounge grant money to make up the bulk of your salary while the clinical track pathologist just shows up and diagnoses stuff for theirs. This of course affords you the right to take no call and minimal service work because you're "paying for you own salary" to be there...so long as you keep the grant dollars rolling in. But to answer the question you're probably wondering, and only with rare exception, you'll never approach the earning potential of a private practice pathologist - not even close.
- Will there still be opportunities to go back to the traditional career paths and find a job? In all likelihood, no. Once you've been out of diagnostic pathology for several years, it is very, very difficult to return. The few instances of this I've personally seen or been told about ended very poorly for those pathologists (i.e. fired, resigned, etc.) Once you commit to this path, you're pretty much in it for life unless you get out within a year or two.
