Yes, if you want to keep your bike in Honduras for more than 90 days (renewable for another 90 days in Tegucigalpa) without taking it out of the country for four days and then returning for a new 90 day permit, you need to formally import it and register it in Honduras (or another C-4 country).
You will probably need a tramitador to handle this for you, though I have done it myself with minor help. You should ask your friends around Roatan for who they recommend.
You will need two RTN cards. One is to pay the import taxes, the other is for your vehicle registration. These are taxpayer ID cards. There are requirements for obtaining these cards, but a tramitador with the right connections can make things happen (yes, a little $ helps).
Import taxes on a motorcycle over 250cc are 10% plus 12% plus 5% road fee. But the fun part is that the 12% is paid on the vehicle value plus the 10%. So you pay the 10% tax and then you pay 12% tax on the vehicle and on the 10% you already paid.
But the worst part of the system is that DEI (tax office) has their own values on each vehicle in their computer which may or may not have any relationship to its true market value. And first you have to pay an initial tax which is not refundable, and only after you pay the initial tax will they tell you what the total tax is, and then you make this second payment.
I have imported a Ducati, two Cagiva Gran Canyons, a GasGas FSE, and a Honda XR650R. Each time I have paid around $600 U.S. import tax, but I have often had to fight to get DEI or customs to compromise on a valuation.
You will also need to purchase a poliza form, which costs $120 U.S. plus an additional $22 U.S. filing fee.
There will be a physical examination of the bike's serial #s by DEI.
Lots of lines and trips to the bank to pay fees.
The better news is that once the bike is imported, annual taxes and registration fees are easily paid at the bank and are nominal.
If you run into difficulties, let me know.