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As part of an experiment I cut a Cat 5e Ethernet cable in half, stripped off a small amount of insulation on each wire and attached each pair of wires together with its own alligator clip.

There are four twisted pairs, so eight pairs of alligator clips are used.

Before cutting it in half I am able to transfer data between two computers using the cable and get ~940MBit/s which is close to the Gigabit/s speeds that Cat 5e is cable of.

However, after cutting it in half and reattaching the wires with alligator clips I get a 10x reduction in bandwidth and get a ~94MBits/s

What might be the reason for this and are there any techniques I can use to regain the original 940MBit/s speed.

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    Did the interfaces still negotiate 1Gbit/s? A splice will have an impact, but given the throughput dropped by almost exactly a factor 10 i suspect one or more conductors are not making a connection. 802.3ab (1000BASE-T, 1Gbit/s) requires all 4 pairs while 802.3u (100BASE-TX, 100Mbit/s) is only active on 2 pairs. Put a cable tester on the patch cable and let us know.
    – MerlinTheMagic
    Commented Jun 11, 2017 at 12:05
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    The standard is ANSI/TIA/EIA 568, Commercial Building Telecommunications Cabling Standard, and it explicitly forbids splices in cabling. You cannot get a cable to pass the category test suite with a splice. Modern networking frequencies require a lot more than simple electrical connectivity. You will introduce all types of problems from crosstalk to impedance mismatches to decreasing the return loss.
    – Ron Maupin ♦
    Commented May 26, 2018 at 1:28

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This is more or less to be expected - alligator clips aren't Cat anything, so probably the link training gave up and the link fell back to Fast Ethernet (not standard but not uncommon). Another possibility is that there's a bad contact somewhere and one of the pairs didn't link, also causing a fallback to FE.

If you can't replace the cable, use a splice box to reattach the ends. Cat5 splice box

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    Punchdown connections like you show in your picture are only suitable for solid cable. If it is stranded you are likely better off crimping plugs on and using a coupler.
    – Peter Green
    Commented Jun 15, 2017 at 18:40
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Each pair of conductors is a transmission line. When you untwist and reconnect the conductors you create discontinuities in the line impedance at the point of the splice which can result in line reflections (results in sharply defined pulses becoming "blurry") and radiation or reception of noise. If the network devices at each end begin seeing signal errors (which would be caused by the above) they automatically shift down (negotiate) to the next lower standard speed to maintain connectivity and reduced data errors.

Great experiment!

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    Transmission errors do not cause a fall back to a lower speed generally with Ethernet. Only when the PCS sublayer fails to establish a proper 4-pair link for 1000BASE-T do some devices (most notably Broadcom) fall back to 2-pair 100BASE-TX.
    – Zac67 ♦
    Commented Mar 16, 2021 at 16:48

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