First, like the others have mentioned you have no bridging loop here due to running a Portchannel. That said, running STP is still fine. Let me clear some confusions on how these commands work on Cisco switches.
spanning-tree portfast trunk
This command is supposed to be run on trunk ports towards non bridging devices, such as a server with multiple VLANs or a router. This command should not be run on trunks towards switches because the port will bypass the listening and learning phase which could potentially create a bridging loop.
If you have an interface configured like this:
interface x/x
spanning-tree portfast
spanning-tree bpdufilter enable
spanning-tree bpduguard enable
BPDU guard will never kick in because BPDU filter is filtering both the outgoing and incoming BPDUs. This also means that the port can never lose its Portfast status which it would normally do if BPDUs were received inbound. If you remove the filter then BPDU guard will kick in and shutdown the port if a BPDU is received. This is done before the port can lose its Portfast operatational state so basically the port will always operate in Porfast operational mode.
If you apply the commands globally instead:
spanning-tree portfast default
spanning-tree portfast bpdufilter default
spanning-tree portfast bpduguard default
The first command enables Portfast on all access ports.
When BPDU filter is applied globally, the difference is that it sends out 11 BPDUs before going silent. Because normally one BPDU is sent out every 2 seconds and the default MaxAge is 20 seconds that means that if there is a device at the other end that can process BPDUs, at least one BPDU would be received when the old BPDU (if there was one) has expired.
If a BPDU is received inbound when BPDU filter is applied globally then the port stops filtering and it will lose its Portfast status.
The BPDU guard default command will only apply to ports that are in a Portfast operational state.
If you combine these three commands together then what will happen is that when a BPDU is received the port loses its BPDU filter, BPDU guard can then kick in. The port will never lose its Portfast operational state because the port is shutdown before.
So you see when applied to the interface BPDU guard can never kick in but if you apply it globally it can.
If you run just Portfast globally and BPDU filter globally then if a BPDU comes in, the port loses the filter and loses the Portfast operational state and will operate as a normal port.
Use spanning-tree portfast, and spanning-tree bpduguard enable on each switchport. Root guard is unnecessary on ports with this configuration, because bpduguard will err-disable the port when you receive any bpdus.
Use root guard on links to other switches, which are not planned for the primary or secondary stp root role.
Best Answer
You cannot modify STP hello timer only for one port - it is timer for whole STP tree. Also this modification wil not help you - because if you have drops on this long link, you will have problem with STP anyway.
What you need to do?
If you have only one link, you can turn off STP for the both side for this link and split STP to two domains (one domain per site). You can do this by "bpdugilter" on the both sides of this link. In this case you can also implement a storm-control\any other protection for this link to be sure that problem in one site will not propogated to other site.
If you have two links between these places (for redundancy), you definitely need to avoid any L2 protocols between them. You need to implement IP routing and then, if you need Ethernet between two segments in the different sites, you can implement tunneling.
My experience say me, that the best answer in such case is MPLS, but maybe you cannot do this due to budget/equipment limitation.