The responses here so far have been great. I'm mostly just gonna reiterate what others have said.

First off, give him a preliminary proposal breaking down the costs and possible options. I've got one that's the starting point for any cabinets I build. Was gonna post it earlier, but then had to head out and do some finishing setup work on a cabinet and now I'm not at home with access to it. I'll get it posted here tomorrow. Anyways, I break stuff down into the major components and list any possible upgrades.
Usually a flat fee for the cabinet materials which runs ~ $200.00 That includes all wood, fasteners, paint, marquee acrylic & backlight, T-molding, etc. Probably a good 50 - 75% higher than my actual costs.
Controls are listed for a basic 4/8-way switchable 2-Player 6/7 button layout with an I-Pac. Optional 3 & 4 player controls, trackballs, spinners, etc are listed with their corresponding price. I typically don't charge much (if any) over actual cost for the controls.
List the price of various TV / monitor options.
If the computer isn't supplied, current market prices for a decently powerful system is listed with the notation that a computer that would play some of the newer games will require an additional cost while one built soley for the classics will be less. When you're pricing a system, remember everything that's involved if you're not buying one already assembled. You'll need motherboard, processor, memory, hard drive, video card, power supply and (unless you're gonna gonna leave the custome without any self-upgrading options) keyboard, mouse, & CD-rom drive.
Artwork design can get expensive. I offer some generic stuff for essentially the cost of printing, but custom work is gonna be more costly. I've got little in the way of artistic deisgn skills, so this gets subcontracted out to my girlfriend. And she's
not cheap.
Finally my design/construction/setup fees work out to about $20-$25 an hour. I've typically charged right around $500 for my fees. Realistically, I shortchange myself here as I've only ever built custom cabs from scratch (instead of converting an existing cabinet) and spend
alot of time in the design phase. I find it enjoyable though, so I really don't charge for more than a coupla hours design time. Setup time is probably also more actual time than I charge for, but that's including stuff like installing the OS on the computer and whatnot. I'm always working on stuff of my own while that's going on in the background. I also state that the cabinet will be delivered and set up in a fully working condition. Any service/upgrades that are required after I leave the first day are charged at $25 an hour plus travel expenses (unless there's something wrong that's my fault.)
I'll get the prospective customer this preliminary proposal along with some 3D renders and pictures of cabs I've built. As well as a list of games with control needs that aren't covered by the basic 2P/6 button layout. I'll then schedule a sit-down with them (preferrably at their place so I can get measurements and such) and discuss their needs/wants in detail. Hafta have 4-Players for Gauntlet? Love Missle Command?
HAVE to roll some two-player Marble Madness? Want an old school cabinet where the CP doesn't extend past the edges? Space restrictions? What's the desired delivery date? Is that feasible? Will the client be providing any of the necessary parts (computer? TV? controls?)?
All of this results in a official contract and
has to be hashed out ahead of time. If changes are made along the way, they should be documented and signed off on by both parties as well. I do this for
every job I ever do, even for friends. It's the best way to
remain friends. Makes sure you both know exactly where things stand. (I'm not so uptight with my closest friends, but anyone who's a casual friend or less calls for a formal agreement.)
FWIW, every cabinet I've built from scratch has ended up costing the client in the realm of $1,500.00 US.
A few words of advice. If you have a specific delivery date, allow a coupla days cushion. Don't expect to be slapping the thing together and delivering it that afternoon. Invariably, there's a setup problem with the computer. (I spent 2 weeks hashing out problems on the last one I built due to using an existing computer that I couldn't format and do a fresh install on. Just as I got it all straightened out, the client decides to go ahead and buy new components for me to assemble him a more powerful one. Got it thrown together with a fresh Win 98 install and everything set up nicely overnight. Took it out and replaced the existing system with it this afternoon. I forgot the S-video to RCA adapter that I needed, so I decided to swap in the card from the old system for the time being. Unfortunatly, loading the drivers for the replacemement card crapped the whole system. So now he's without it for a few days until I can get home & rebuild it
again.) Or there's a bad controller (This
same cabinet has a faulty I-Pac4. The P1-B2 input started going spotty immediately after assembly and eventually quit alltogether. Not a devastating problem, as I had some spare input slots open and just moved the wire & reprogrammed the I-Pac, but it could have caused alot more trouble than it did.) Or you've run out of wire after the stores have closed. Unexpected delays are probably more the norm than the exception with projects such as these.
Good luck.