First off, you'll find out soon enough that Apache config files changes and connecting an app to the MySQL database is not programming.
The hard part about web based app design is learning how to write SQL queries and code that is efficient. There can be a lot of ways to get the same data out of a table, but some may result in the server killing itself if 100+ people hit the site at the exact same time.
How hard is the transition between job types? I think it depends on the analyst job. "System Analyst" is just a generic term. I am one, but my job is mostly web server admin with a bit of coding. Our apps are all internal, so any PHP coding I do doesn't have to be super awesome efficient, just get the job done. We have 3 other PHP coders, and they are good, but I still see some buggy stuff being created.
I guess it really depends on what the company expects. If they expect top of the line coding, then the transition to a programmer job will be harder and require more time in training. I'll even go so far as to say you really need a full Computer Science degree to have the proper background knowledge about to be a really good programmer. If they just want a hack coder to get something working for a limited time, then it's not very tough really and can be done with minimal training...
I hope I actually helped. I think the biggest concern you should have right now is if you will actually like doing web based programming. It can become tiresome if you spend enough 8 to 10 hour days in a row staring at a computer screen writing PHP code. You may want to go buy some PHP/MySQL books and think up a couple app ideas and try to write them on your own. At least to see what it's like before switching jobs.
I went the opposite direction as you, started as a desktop tech, got my degree, thought I wanted to be a programmer. After about a year and a half of coding I got tired of it and wanted to move more towards an admin position of some sort. So far so good.
edit: Sorry if any of this comes across as mean. I don't intend it to be, just trying to be helpful and provide some of my personal experience in the field.