Is this an alignment issue or something else?

The initial post cut off part of it:

Satellite transponders (14 total at 99º(cb))
1-8 0 89 0 89 0 86 0 89
9-16 0 88 0 87 0 86 NA NA
17-24 NA NA NA NA NA NA NA NA
25-32 NA NA NA NA NA NA NA NA
Signal Strength Not Acquired

Satellite transponders (16 total at 103º(ca))
1-8 87 82 88 82 88 79 85 76
9-16 90 83 89 80 86 79 85 83
17-24 83 81 84 81 83 82 84 79
25-32 NA NA NA NA NA NA NA NA
Signal Strength 88%

Satellite transponders (14 total at 103º(cb))
1-8 86 82 83 80 83 85 82
9-16 83 82 83 84 85 82 NA NA
17-24 NA NA NA NA NA NA NA NA
25-32 NA NA NA NA NA NA NA NA
Signal Strength 88%

Satellite transponders (18 total at 99º(s))
1-8 0 57 0 58 0 99 0 96
9-16 NA NA NA NA NA NA 0 0
17-24 0 92 0 0 0 53 0 86
25-32 NA NA NA NA NA NA NA NA
Signal Strength Not Acquired

Satellite transponders (10 total at 103º(s))
1-8 NA NA NA NA NA NA NA NA
9-16 NA NA NA NA NA NA 0 74
17-24 95 92 80 75 90 91 0 0
25-32 NA NA NA NA NA NA NA NA
Signal Strength Not Acquired

I've visually inspected the cable and it's appears to be fine.  The dish has not moved and there isn't anything blocking the signal.  Wanted to ask here before I started to do anything with the alignment, in fear that I messed it up when the issue was hardware.  Thanks

If out of alignment then dish may have moved (such as what it is attached to shifted). May be very slight to where it is not obvious (as nobody stares at their dish 24/7 making note of minute changes), but just enough to start affecting signal.

Also if you have the HR34, that is another concern. That would be the 1st generation Genie which is well known for slowness problems and heating issues. The 2nd/3rd generation Genies were made with a faster processor and redesigned for more efficient cooling. If needed you can also call DirecTV and let them know it is dead to get it a warranty replacement shipped for an HR44 or HR54 (depending on stock).

If you do replace that HR34 be aware that recordings do not transfer so be comfortably caught up. Also if it matters, phone jack is no longer used (no longer exists starting with HR54). And if you use a wireless CCK to connect to your home internet, that will be unplugged as the newer ones have it built-in (supporting not just 2.4GHz but 5GHz as well).

You've lost all the odd transponders on the 99 satellites. This is either a cable/connector issue, or (less likely) an LNB. 

Dou you have the "legacy" dish with four cables to the house, or is it an SWM system (one cable to the house)??

Do you have multiple receiver and does the same problem exist withe just one box?

This is an SWM system, one cable running to the house and the issue is identical on all receivers.  I had to recheck that as I could not recall.

Is this possibly the cable running from the disk switch that is in my basement? 

What disk switch?

For an SWM system with good signal on the even 99 transponders and no 99 odd signals on all the receivers  it's virtually impossible for this to be a cable issue. Almost certainly the LNB at the dish is faulty.

What are the models of those other boxes?