From what you tell me this sounds like a hardware defect or that no 
IR light reaches the built-in sensor anymore. Why?

1) The only thing that happened between working state and non-working 
state was the hardware disassembly / assembly. The software didn't 
change and it worked before. Result: this is a hardware problem.

2) You can't bring up the boot menu with the Apple Remote. This 
feature is implemented in the EFI firmware. So this is a feature 
running at a point where OS X hasn't even started running yet. 
Consequently, this feature is completely outside of the sphere of 
influence of any software (including Remote Buddy, which can't cause 
you such a problem anyway). Result: this is a hardware problem.

3) You reset the PRAM, which - with Apple hardware - is sometimes 
necessary to cure a USB problem (the IR receiver is internally 
connected via USB), when OS X no longer sees an actually connected 
device. Result: this is a hardware problem.

4) The Apple IR receiver hardware as such seems to be detected on the 
USB bus as such (you wouldn't see it in Remote Buddy otherwise). Which 
can still mean that a component of the receiver is defective after the 
hardware assembly/disassembly, but at least there's a chance that you 
just didn't put it back into its place correctly and that there's now 
no longer a line of sight between the receiver's IR sensor and the 
"outside world". Result: this is a hardware or physical problem.

5) The EyeTV receiver has nothing to do with the built-in Apple IR 
receiver. The EyeTV receiver is a completely independent IR receiver 
built into your EyeTV-supported hardware, that can *also* be used with 
Remote Buddy. More info on this on the Remote Buddy website point 
"EyeTV remotes". Result: the EyeTV receiver has no relevance to this 
problem.

My resumée:

Your problem IS a hardware (or physical, and thus also hardware) 
problem. It is not a software problem. Remote Buddy has no part in it. 
Nor has OS X. Uninstalling or reinstalling any software - be it Remote 
Buddy or be it OS X itself - will not solve the problem.

Best regards, 
Felix Schwarz