Few Issues After Rooting

I believe that paid apps are the only ones that are supposed to come back automatically. I use Titainium or MyBackupPro to reinstall the missing apps.
I don't think its a problem with BB.

I don't know about the alarm clock...I don't think I have that issue. I use it pretty frequently. Maybe you should wipe and reinstall.

 

For future reference questions like this should probably go in the hacking discussion or the specific section relating to the rom your using. Now on to your questions:

1. I had this problem too once or twice even though pete said that he didnt disable this feature, I feel your pain as I have about 130 apps. I ended up just restoring them from /data that I had saved.

2. The only thing that I can think of is maybe a task killer is killing the app? I have the multimedia dock so my phone is always on at night and I never have a problem with it. What alarm clock app are you using?

You are incorrect sir, they all (should) come back

 

If you want to keep a list of all the apps you downloaded check out appbrain, it will allow you to keep lists of apps and sync them between your android device and your pc but it wont do auto installations

I use gentle alarm by default, but use the "clock" app when its in the dock ive used it when gentle alarm wasnt installed and it still seems to work fine. Maybe try another app and see if you have the same problem.

 

To ensure that all of my market apps restore after a ROM here's what I do. First, before installing a new ROM I make sure that both "Back up my data" and "Automatic restore" are checked in the phone's Privacy settings. If they weren't both already enabled, wait a while after you've enabled them before installing the new ROM; in fact, force a sync by turning off auto-sync and turning it back on.

If you're already rooted, then try Titanium Backup to back up all of your apps, data, & system settings.

After the new ROM is installed and you've logged into your Google account then JUST WAIT AND LEAVE THE PHONE ALONE. Some ROMs disable the setup wizard, but you can just open the Market app and connect to your Google account. If you open the Market app, JUST WAIT AND LEAVE THE PHONE ALONE. If you go into and Market app and exit it, or force close it, then you may not get all of your free apps restored. When you first set up your Google account on the phone you'll see the sync icon in the top taskbar. It will go away after a few minutes, but that does NOT mean that it's done downloading the apps. Continue to wait. You should eventually get a notification that your apps were restored. I'd wait up to 20 minutes if I didn't already get the notification.

When I installed BB.4 my apps showed "free" instead of "installed" on the download page of the market. I forced close the Market app, then clearead its cache & data, then ran the Market Doctor from Titanium Backup, and rebooted the phone. That took care of it.