Ok , step back , remove the relays; you re-located completely , and re-assess the issues .
Fuses are usually on the input voltage to the relays and if your blowing fuses ;they should blow before the relay is damaged.
You mentioned 3 circuits; marker , brake and signals . So you blow 3 fuses ?
Are these fuses blowing , without activating the lights involved , or after trying to activate?
I've been involved with some members who have problems with an Arens shifter for the Allison 2100/2500 series transmissions .
What engine and transmission do you have in your coach ?
Do you loose shift pad read out when the fuses blow ?
99DSDP 3884, Freightliner, XC, CAT 3126B, 300 HP /ALLISON 3060
2000 Caravan toad, Remco & Blue Ox.