It looks like you are asking if there's a standard template to use to answer these questions. Having spent years in consulting, I can tell you that the answer is generally "no."
Since the client specifically asked for responses in those areas, I would make sure to include sections that correspond to those areas.
Implementation timeline: Make this a relatively high-level Gantt chart with milestones. Highlight key delivery dates. Use this as an opportunity to show that you understand the software development lifecycle, and use it as an opportunity to communicate to the customer what SDLC methodology you will be using.
Costs: Remember time and expenses. Break it down by whatever slice-and-dice the customer is expecting. If it's full time & materials, give them number of hours times hourly rate. If it is flat fee, give them one number, but explain to them what they're getting by major deliverable (just make sure they don't expect to be able to smorgasbord the features and get a different price).
Functionality: Communicate to them what they're getting for their money. Which major features are in scope, and which are out of scope. Depending on the size of the organizations on both sides of this deal, there's a very real possibility of the proposal becoming the contract. Make sure you spell out very clearly what you will deliver for the agreed-upon price.
Tech support: Be simple and clear here. Once you've delivered the software, if they need help or changes, how do they get them, and how much will they cost. Do not sell yourself short on this part. Clients always find new features, and do a great job finding bugs five years after the software is delivered. Also, make sure you expressly define your warranty here.
Structure of the proposal should probably be in this order: Functionality, Timeline, Tech Support, Cost. Overall, though, the order of these items doesn't matter a whole lot.
CAVEAT: If the client has given you a format in which they want you to respond, use that format! I've had a lot of RFPs that I've sent out that specifically state for the vendor to use the approved format, only to have a provider-branded PDF come back that has me scrambling to find answers to critical questions that have been scattered throughout their response. It's annoying, and has caused more than one potential vendor to make it to the bottom of my list.
Another caveat: If you are responding to a governmental RFP, re-read the above caveat and repeat to yourself: "I will respond in the format they require."