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CAT5 Wiring in Wall too Short to reach Patch Panel - Best Solution???

I ran into an issue after taking over a Network Admin job at a local company. Turns out the guy before me ran wiring from the wall directly into a switch, with no patch panelling whatsoever inbetween. Needless to say this is ridiculous and makes it hard to troubleshoot and change things.

I am trying to move the cabling over to a patch panel in the local area but the wiring does not have enough reach (a bundle of about 20 wires) - all about 3 feet short. Is it okay to just connect short 3 feet lengths of CAT5 to these wires to make the right length? Or will there be signal loss or other complications?

I'm trying to avoid rewiring everything in the walls.  Is there any way I can extend these wires safely and reliably?
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Remember, with every connection you place in the line you will have a signal degradation by way of lost signal and introduced noise or magnetic interference.
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Well its about 20 drops total, and the wire lengths run up to 50-60 feet, not too terrible.  I had a feeling that spliced connection would add interference.

I've seen a few already done in this building using this method:
Both wires are capped with plugs, and then the old Admin used a female-to-female connector for the CAT5 and plugged them into each other.

I'm assuming that also adds interference and noise?
Question : while I'm doing this, should I just rewire the area for CAT 6?  Or would that have issues with the rest of the CAT5e in the building?  Is this the type of thing you do all or nothing?  Or could installing CAT 6 in this part of the building just function like CAT5e until the rest of the building is wired as well?
Well, cat5e can do 1Gbps out to 100m; cat6 can do 10Gbps for short distances; cat6a supports 10Gbps out to 100m.

Cat7 is supposed to support 100Gbps out to 100m, but it's not an official spec yet... not expected until 2012 at least.
So if you're going to rewire, the best you can do currently is cat6a, and that should have you ready for 10Gb when the prices on those come down.

The tools to certify the runs will likely cost you more than the four 1000' spools of cat6a Riser or Plenum will.
>>> Or would that have issues with the rest of the CAT5e in the building?

You can mix Cat5e and 6 at will on separate cable runs; they will not interfere with each other.  You do not have to replace lines that do not need it; though if you are going to upgrade the wires, you might as well do them all at once - as permissible by budget.  Then you don't have to worry about it in the future.
The area I'm rewiring is a remote part of the building connected to our main server via a Trunk port. It's only about 20 runs in the local area that are capped with plugs and literally plugged directly into the switch. My switch is facing backwards because there is no slack and I cannot see or make changes to this, kinda stupid.

What tools would I need to certify CAT6 runs or any of that?  
To just check continuity between pins, testers are available for under $100... that may be suitable for home/hobby use, but not for professional/industrial installations. :-|

You may be able to get by with a cable qualifier if your company doesn't require certification (yet).
e.g. http://www.provantage.com/fluke-networks-ciq-kit~7FLUK0AA.htm

This is the least expensive certifier I know of:
http://www.testequipmentdepot.com/testum/testver/nt950.htm for gigabit

But you can spend upwards of $10k for top-notch name brand equipment that does fiber too, e.g.
http://cableorganizer.com/fluke-networks/fluke-dtx.htm (the 1800 certs cat6a to 10Gb too)